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Zucchini Bagels (Low Carb, Keto) – The Ultimate Low Carb Breakfast
I still remember the first time I made these low carb zucchini bagels. It was a rainy Tuesday in my tiny Paris apartment, years before I ever set foot in a New York City kitchen. I had just come home from a long pastry shift at Le Cordon Bleu, craving something chewy and satisfying—but also something that wouldn’t derail my low carb lifestyle. My mom back in Morocco used to grate zucchini into everything: tagines, pancakes, even bread. So I thought, why not bagels? That first batch was far from perfect, but it sparked something. Now, after years of testing and tweaking, this keto bagel recipe is one of my most-loved creations on cheerychop.com. It combines the best of my worlds: the resourcefulness of my Moroccan mother’s kitchen, the precision of French pastry training, and the bold, grab-and-go energy of NYC food culture.
Let me paint you a picture: the moment these keto zucchini bagels come out of the oven, your kitchen fills with the toasty, nutty aroma of melted mozzarella and golden coconut flour. The tops are speckled with everything bagel seasoning—sesame seeds, poppy seeds, dried garlic, and onion flakes—crisping up into the most irresistible crust. When you cut one open, the interior is tender and pillowy, with a slight springy chew that rivals any traditional bagel. There’s no grittiness, no wetness, no eggy taste—just pure, comforting bagel goodness. Each bite carries a whisper of zucchini, but in the best way: it adds moisture and tenderness without yelling “I’m a vegetable.” I like to toast mine lightly and slather it with scallion cream cheese. It’s the breakfast I didn’t know I needed, and now I can’t imagine my NYC mornings without it.
What sets this low carb bagel with coconut flour apart from other keto bagel recipes is the technique. I use coconut flour instead of almond flour—and I’ve perfected the ratio so you get a soft, bagel-like crumb, not a dry or crumbly mess. Plus, I’ve cracked the code on preventing soggy zucchini bagels (it’s all in the squeeze, my friends). This recipe uses just six simple ingredients: zucchini, mozzarella, coconut flour, baking powder, eggs, and everything seasoning. No weird gums, no hard-to-find flours. I’ll walk you through every step, including the one common mistake most people make when working with zucchini, so you can nail these on your first try. From my NYC kitchen to yours—let’s make some bagels.
Why This Zucchini Bagels Recipe Is the Best
The Flavor Secret: Most low carb bagels taste like eggy cardboard. Not these. The secret is the combination of low-moisture mozzarella and coconut flour. The mozzarella melts into the batter, creating a rich, savory foundation that mimics the chew of wheat gluten. The coconut flour, which I learned to work with in Paris, adds a subtle sweetness and a light, tender crumb. Together, they create a bagel that’s actually delicious on its own—no cream cheese required to hide the taste. Plus, that everything bagel seasoning on top isn’t just for show; it bakes right into the surface, creating a crunchy, aromatic crust that will transport you straight to your favorite NYC deli.
Perfected Texture: The biggest challenge with keto bagels is getting that bagel-like chew without gluten. In my Paris training, I learned how different fats and proteins interact to create structure. Here, the mozzarella provides the protein matrix, while the coconut flour absorbs moisture and adds structure. The eggs bind everything together. But the real game-changer? Shredding the zucchini finely and squeezing it DRY. I mean, really dry. This step removes excess water that would otherwise turn your bagels into sad, soggy discs. My technique yields a bagel that’s chewy on the outside, tender on the inside, and holds up to toasting, slicing, and schmearing.
Foolproof & Fast: I’ve tested this recipe at least a dozen times (bless my neighbors, who got many experimental bagels shoved through their doors), and I’ve simplified it so anyone can make it. You don’t need a stand mixer, a piping bag, or any special equipment. Just a box grater, a clean kitchen towel, and a baking sheet. The entire process takes about 35 minutes, and most of that is hands-off baking time. Even if you’ve never made a keto bagel before, my step-by-step instructions and pro tips will guide you to perfect results. Trust me—if I can make these in my tiny NYC apartment kitchen with a 30-year-old oven, you can make them anywhere.
Low Carb Zucchini Bagels Ingredients
I pick up my zucchini at the Union Square Greenmarket in NYC during the summer, but good-quality supermarket zucchini works beautifully year-round. The key is to use firm, medium-sized zucchini—not the giant ones that are mostly seeds and water. The mozzarella I use is the low-moisture block style (not fresh mozzarella), which melts perfectly and adds the right chew. And the coconut flour—I get mine from Thrive Market or any well-stocked grocery store. It’s important to use coconut flour here, not almond flour, because coconut flour absorbs much more liquid, which is exactly what we need to balance the moisture from the zucchini.
Ingredients List
- 3 cups zucchini, finely shredded (about 2 medium zucchini)
- 1½ cups low-moisture shredded mozzarella cheese (about 6 oz)
- ⅓ cup coconut flour
- 1 tsp baking powder
- 2 large eggs
- Everything bagel seasoning, for topping (about 2 tbsp)
Ingredient Spotlight
Zucchini: The star of these low carb zucchini bagels. Zucchini adds moisture and tenderness without adding many carbs. Use the fine holes of a box grater (not the large ones) so the zucchini blends seamlessly into the batter. After shredding, you’ll need to squeeze out as much liquid as possible—I’ll show you exactly how in the steps. Tested substitution: Yellow summer squash works perfectly in place of zucchini. No other substitution is recommended.
Coconut Flour: This is the key to making these bagels both low carb and nut-free. Coconut flour is extremely absorbent, which means a little goes a long way. It gives the bagels a light, tender crumb that’s very different from the denser texture of almond flour. Tested substitution: You can use almond flour, but the texture will be denser and more oily. Use 1 cup almond flour in place of the ⅓ cup coconut flour. The interior will be softer and less bread-like. Do not substitute with any other flour (not wheat, oat, or cassava) as the carb counts will increase.
Low-Moisture Mozzarella: This is the backbone of the bagel’s structure. When melted, mozzarella becomes stretchy and pliable, creating a protein network that mimics gluten. It also adds a savory, milky flavor that pairs perfectly with the everything seasoning. Tested substitution: Part-skim or whole milk low-moisture mozzarella both work. Avoid fresh mozzarella (too wet) or pre-shredded bagged cheese (adds anti-caking agents that affect texture). You can substitute with provolone or gouda for a different flavor, but mozzarella gives the best neutral base.
| Original Ingredient | Best Substitution | Flavor / Texture Impact |
|---|---|---|
| Zucchini (3 cups shredded) | Yellow summer squash | Very similar; slightly less green color, same moisture content. |
| Coconut flour (⅓ cup) | Almond flour (1 cup) | Denser, richer interior; more fat and calories, still low carb. |
| Low-moisture mozzarella | Provolone or gouda | Slightly sharper flavor; similar melt and chew. |
| Everything bagel seasoning | Sesame seeds + flaky salt + dried garlic | Homemade mix works; adjust salt to taste. |
How to Make Zucchini Bagels — Step-by-Step
Making these low carb zucchini bagels is simpler than you think. Follow these steps, and you’ll have a batch of golden, chewy, keto-friendly bagels ready in under 40 minutes.
Step 1: Preheat and Prepare
Preheat your oven to 400°F (200°C). Line a large baking sheet with parchment paper. This is important—the bagels will stick to foil or a silicone mat if not properly lined. I like to use unbleached parchment paper; it’s sturdy and nothing sticks.
💡 Sara’s Pro Tip: For extra-crispy bottoms, flip the baking sheet upside down and bake the bagels directly on the inverted sheet. The heat circulates better and you get a more even golden crust.
Step 2: Shred and Squeeze
Wash the zucchini and trim off the ends. Using the fine holes of a box grater, shred the zucchini into a large bowl. You should have about 3 loosely packed cups. Now—and this is crucial—transfer the shredded zucchini to a clean kitchen towel or a nut milk bag. Gather the corners and twist tightly over the sink, squeezing out as much liquid as you can. You’ll be shocked how much water comes out. Keep squeezing until barely any liquid remains. This is the secret to non-soggy zucchini bagels.
⚠️ Common Mistake to Avoid: Skipping the squeeze or using paper towels instead of a kitchen towel. Paper towels will disintegrate and leave lint on your zucchini. A sturdy kitchen towel or nut milk bag is essential. And don’t just press—really wring it out. Your bagels will thank you.
Step 3: Melt and Mix
In a medium microwave-safe bowl, combine the shredded mozzarella and the squeezed-dry zucchini. Microwave in 30-second bursts, stirring in between, until the cheese is fully melted and the mixture is hot and cohesive (about 60–90 seconds total). Let it cool for 2 minutes so you don’t scramble the eggs. Then, add the coconut flour, baking powder, and eggs. Stir vigorously with a silicone spatula until a thick, sticky dough forms. The dough will be very pliable and slightly tacky, not dry.
💡 Sara’s Pro Tip: If the dough seems too wet, add 1 more tablespoon of coconut flour and mix again. If it seems too dry, add 1 teaspoon of water. Humidity and zucchini moisture vary, so trust your hands more than the clock.
Step 4: Shape the Bagels
Lightly wet your hands with water (this prevents sticking). Divide the dough into 6 equal portions, about ⅓ cup each. Roll each portion into a ball, then poke a hole in the center with your thumb. Gently stretch the hole to about 1 inch in diameter, shaping it into a bagel ring. Place each shaped bagel on the prepared baking sheet, spacing them about 2 inches apart. Sprinkle the tops generously with everything bagel seasoning, pressing lightly so it sticks.
⚠️ Common Mistake to Avoid: Making the holes too small. The holes will close up during baking, so make them larger than you think—about the size of a quarter. If you skip this, you’ll get bagel-shaped rolls instead of proper bagels.
Step 5: Bake to Perfection
Bake at 400°F for 18–22 minutes, or until the bagels are golden brown on top and feel firm to the touch. The bottoms should be browned and crisp. Let them cool on the baking sheet for 5 minutes, then transfer to a wire rack to cool completely. The texture firms up as they cool, so don’t skip this step. Serve warm or at room temperature.
💡 Sara’s Pro Tip: For an extra-crusty exterior, turn on the broiler for the last 1–2 minutes of baking. Watch closely, as coconut flour browns quickly. This gives the bagels that coveted bakery-style crunch.
| Step | Action | Duration | Key Visual Cue |
|---|---|---|---|
| 1 | Preheat oven & line baking sheet | 5 min | Oven at 400°F, parchment ready |
| 2 | Shred & squeeze zucchini dry | 6 min | No visible water dripping from towel |
| 3 | Melt mozzarella with zucchini, mix dough | 4 min | Cheese fully melted, dough thick and sticky |
| 4 | Shape into bagels with thumb hole | 4 min | 6 even rings, hole ~1 inch wide |
| 5 | Bake until golden and firm | 20 min | Golden brown tops, firm to touch |
Serving & Presentation
These low carb zucchini bagels are incredibly versatile. I love serving them halved and toasted (just 3–4 minutes in a toaster or under the broiler) with a generous schmear of scallion cream cheese. In the summer, I top them with smoked salmon, capers, and a squeeze of lemon—a nod to the classic NYC bagel experience that made me fall in love with this city. The slight sweetness from the coconut flour balances beautifully with savory toppings. For a Moroccan-inspired twist, I sometimes serve them with labneh (strained yogurt) and a drizzle of harissa oil. It’s unexpected, but the creamy, spicy combo is absolutely addictive.
For presentation, I arrange the bagels on a wooden board with small bowls of toppings: cream cheese, butter, smoked fish, sliced avocado, and fresh herbs. It makes for a stunning brunch spread that looks as good as it tastes. These bagels are also perfect for meal prep—I make a batch on Sunday and enjoy them all week. Just slice them in half before storing, so they’re ready to toast and go.
| Pairing Type | Suggestions | Why It Works |
|---|---|---|
| Side Dish | Mixed green salad, roasted cherry tomatoes, cucumber slices | Light, fresh sides contrast the rich, chewy bagels. |
| Sauce / Dip | Scallion cream cheese, labneh, avocado mash, smoked salmon spread | Savory creamy toppings complement the neutral, toasty bagel flavor. |
| Beverage | Black coffee, iced matcha latte, fresh orange juice, mint tea | The bitterness of coffee and green tea balances the richness of the bagels. |
| Garnish | Everything bagel seasoning, fresh dill, microgreens, flaky salt | Adds crunch, color, and a finishing touch of flavor. |
Make-Ahead, Storage & Reheating
As a busy NYC food blogger and mom, I live by make-ahead strategies. These keto bagels are perfect for meal prep. I bake a double batch on Sunday, and we enjoy them for breakfast all week long. The key is storing them properly so they stay fresh and never get soggy. Here’s my tried-and-true system:
| Method | Container | Duration | Reheating Tip |
|---|---|---|---|
| Refrigerator | Airtight container with paper towel layer | Up to 5 days | Toast halved bagels at 350°F for 5 min, or use a toaster for 3–4 min |
| Freezer | Freezer-safe zip bag, as much air removed as possible | Up to 3 months | Thaw at room temp 15 min, then toast directly from thawed state |
| Make-Ahead | Baked and halved, stored in fridge | 5 days in advance | Toast from chilled; no need to bring to room temp |
One thing I’ve learned the hard way: never store these bagels in a sealed container while they’re still warm. The steam will make the tops soggy and the everything seasoning will lose its crunch. Let them cool completely on a wire rack—about 30 minutes—before storing. If you’re freezing them, I recommend slicing them in half first, then wrapping each half individually in plastic wrap before placing in the freezer bag. That way you can pull out exactly as many halves as you need without defrosting the whole batch.
Variations & Easy Swaps
| Variation | Key Change | Best For | Difficulty Impact |
|---|---|---|---|
| Cheesy Garlic Herb Bagels | Add 2 tbsp grated Parmesan + 1 tsp garlic powder + 1 tbsp dried parsley | Savory lovers, Italian-inspired breakfast | None — just mix into dough |
| Dairy-Free / Vegan Option | Replace mozzarella with 1½ cups shredded vegan mozzarella (violife or miyoko’s) + 1 tbsp nutritional yeast | Dairy-free or vegan diets | Slightly trickier — vegan cheese melts differently |
| Spicy Moroccan Harissa Bagels | Add 1 tbsp harissa paste + ½ tsp cumin + ½ tsp smoked paprika to dough | Bold flavor, North African-inspired twist | None — just adds spice |
Cheesy Garlic Herb Bagels
This variation is inspired by my Paris days, when I’d grab a pain à l’ail (garlic bread) from the boulangerie on my way to class. The combination of Parmesan and garlic is simply irresistible. Mix 2 tablespoons of finely grated Parmesan, 1 teaspoon of garlic powder, and 1 tablespoon of dried parsley into the dough along with the coconut flour. Top with the usual everything seasoning. The Parmesan adds a salty, nutty depth that makes these bagels perfect for a savory breakfast sandwich. I like to stuff them with scrambled eggs and cheddar for a filling keto breakfast that keeps me going through a busy NYC morning.
Dairy-Free / Vegan Option
For my friends who avoid dairy or follow a plant-based lifestyle, I’ve tested this with vegan mozzarella shreds (the brand Violife works best) and it’s surprisingly good. The texture is a bit softer and less chewy than the original, but still very satisfying. Add 1 tablespoon of nutritional yeast to the dough for a cheesy, umami boost. Because vegan cheeses often contain more moisture, you may need an extra tablespoon of coconut flour to achieve the right dough consistency. The bagels will be slightly more delicate, so handle them gently when shaping. They still toast beautifully—the vegan version is a hit in my household on Meatless Mondays.
Spicy Moroccan Harissa Bagels
This variation is a love letter to my Moroccan roots. Harissa is a North African chili paste made with roasted red peppers, garlic, and warm spices. It’s one of the first things I learned to make in my mother’s kitchen in Marrakech, and it’s still my favorite way to add deep, smoky heat to any dish. Stir 1 tablespoon of harissa paste (store-bought is fine, but I’ll share my homemade recipe someday!) along with ½ teaspoon of ground cumin and ½ teaspoon of smoked paprika into the dough. The result is a boldly flavored bagel with a gorgeous reddish-orange hue. I love topping these with a dollop of labneh or Greek yogurt and fresh cilantro. They’re perfect for anyone who likes a little heat with their morning meal.
FAQ
How do you make zucchini bagels without them getting soggy?
The single most important step for preventing soggy low carb zucchini bagels is to squeeze the shredded zucchini extremely dry. After shredding the zucchini on the fine holes of a box grater, transfer it to a clean kitchen towel or a nut milk bag. Gather the corners and twist firmly over the sink, applying steady pressure until hardly any liquid drips out. You’ll be surprised how much water zucchini releases—typically about ½ cup of liquid from 3 cups of shredded zucchini. If you skip this step or don’t squeeze thoroughly, the excess moisture will steam inside the bagels during baking, resulting in a dense, wet, and gummy texture. Additionally, using low-moisture mozzarella (not fresh) and letting the bagels cool completely on a wire rack before storing also helps maintain a firm, bagel-like texture.
Can I substitute almond flour with coconut flour in keto zucchini bagels?
Yes, you can substitute almond flour for coconut flour in this keto zucchini bagel recipe, but the ratio and texture will change significantly. Coconut flour is much more absorbent than almond flour—it soaks up about 4 times more liquid. If a recipe calls for ⅓ cup of coconut flour, you’ll need approximately 1 cup of almond flour as a replacement. Expect a denser, softer, slightly oilier interior texture when using almond flour, compared to the light, tender crumb that coconut flour provides. Additionally, almond flour adds more calories and fat compared to coconut flour. If you’re nut-free or prefer the lighter result, stick with coconut flour. If you only have almond flour on hand, go ahead and use it—the bagels will still be delicious and keto-friendly.
How long do you bake zucchini bagels for a low carb recipe?
For these low carb zucchini bagels, bake at 400°F (200°C) for 18 to 22 minutes. The exact time depends on your oven and the size of your bagels. You’ll know they’re done when the tops are golden brown and the bagels feel firm and slightly springy to the touch. The bottoms should be browned and crisp when you lift one with a spatula. If you’re making smaller or larger bagels, adjust the time accordingly—mini bagels may need only 14–16 minutes, while jumbo bagels could take 24–26 minutes. For an extra-crispy crust, you can turn on the broiler for the final 1–2 minutes, but keep a close eye on them so the coconut flour doesn’t burn. Let the bagels cool on the baking sheet for 5 minutes before transferring to a wire rack.
What are the best toppings or spreads for keto zucchini bagels?
The best toppings for keto zucchini bagels are full-fat, low carb spreads that complement the neutral, slightly savory flavor of the bagels. My top recommendations include: (1) Scallion cream cheese—this is a classic NYC-style choice that pairs beautifully with the everything bagel seasoning. (2) Smoked salmon with capers and a squeeze of lemon—this turns the bagel into a luxurious breakfast or brunch. (3) Avocado mash with salt, pepper, and red pepper flakes—a simple, healthy, and satisfying option. (4) Labneh (strained yogurt) with a drizzle of olive oil and za’atar—a nod to my Moroccan heritage. (5) Butter or ghee with flaky sea salt—sometimes the simplest toppings are the best. All of these are naturally low in carbs and high in flavor.
Are these zucchini bagels truly keto-friendly and how many carbs do they have?
Yes, these zucchini bagels are genuinely keto-friendly. Each bagel contains approximately 4–5 grams of net carbs (total carbs minus fiber), making them an excellent choice for anyone following a ketogenic diet. The main sources of carbohydrates are the zucchini and the coconut flour—both are low in net carbs and high in fiber. The mozzarella, eggs, and everything seasoning contribute negligible carbs. Compared to a traditional wheat bagel (which has about 50 grams of carbs), these keto bagels are a game-changer. For a standard ketogenic diet that limits net carbs to 20–50 grams per day, one these bagels fits perfectly within your allowance. The exact carb count may vary slightly depending on the specific brands of ingredients you use, so I always recommend checking your labels if you’re strictly tracking macros.
Can I make these zucchini bagels without cheese for a dairy-free option?
Yes, you can make a dairy-free version of these low carb zucchini bagels by substituting the mozzarella with a dairy-free alternative. I’ve tested this using shredded vegan mozzarella (the brand Violife works best, but Miyoko’s is also excellent). Use the same amount—1½ cups of shredded vegan mozzarella. Because vegan cheese melts differently and may not provide the same protein structure, the bagels will be slightly softer and less chewy than the original. To compensate, add 1 tablespoon of nutritional yeast for a cheesy flavor, and consider adding 1 teaspoon of psyllium husk powder to help with structure. The dairy-free bagels are still delicious, especially when toasted, and they hold up well for 3–4 days in the fridge. This is a fantastic option for those who are lactose intolerant or follow a vegan keto diet.
Why did my keto zucchini bagels turn out flat and dense instead of fluffy and round?
Flat and dense keto zucchini bagels are usually the result of one of three issues: (1) Not squeezing the zucchini dry enough. Excess moisture makes the dough heavy and prevents it from rising properly. (2) Over-mixing the dough, which can break down the protein structure from the mozzarella and eggs, leading to a dense crumb. Mix just until the ingredients are combined. (3) Using stale baking powder. Baking powder loses its leavening power over time—check the expiration date, and make sure it’s less than 6 months old. To test, drop a teaspoon of baking powder into a bowl of hot water; if it fizzes vigorously, it’s still active. (4) The dough being too warm when shaping. If the mozzarella mixture is too hot, it can make the dough slack. Let it cool for 2–3 minutes before adding eggs and shaping.
Can I freeze these low carb zucchini bagels for later use?
Absolutely! These low carb zucchini bagels freeze beautifully, making them perfect for meal prep. Let the baked bagels cool completely on a wire rack—this prevents condensation from making them soggy in the freezer. Once cool, slice each bagel in half (this makes toasting easier later). Wrap each half individually in plastic wrap, then place the wrapped halves in a freezer-safe zip-top bag. Squeeze out as much air as possible before sealing. They will keep in the freezer for up to 3 months without significant loss of quality. To thaw, simply remove the desired number of halves from the freezer and let them sit at room temperature for about 15 minutes, or pop them directly into a toaster or toaster oven (frozen to toasted in about 4–5 minutes). I recommend toasting from frozen for the best texture—the heat revives the crispy exterior and soft interior beautifully.
What can I use instead of everything bagel seasoning for topping these bagels?
If you don’t have everything bagel seasoning or simply want to try something different, there are plenty of delicious alternatives. The simplest option is a mix of sesame seeds, poppy seeds, dried minced garlic, dried minced onion, and flaky sea salt—these are the components of everything seasoning. You can adjust the ratios to your preference. Other great toppings include: (1) Cinnamon and a low carb sweetener (like monk fruit or erythritol) for a sweet breakfast bagel. (2) Shredded Parmesan cheese mixed with dried oregano—this creates a savory, Italian-inspired crust. (3) Caraway seeds and flaky salt—a nod to classic Jewish deli bagels. (4) Chi seeds and hemp hearts for extra nutrition and a mild, nutty crunch. (5) Smoked paprika and poppy seeds for a colorful, smoky topping. Feel free to experiment!
Are these low carb zucchini bagels gluten-free and nut-free?
Yes, these low carb zucchini bagels are naturally both gluten-free and nut-free when made as written. The recipe uses coconut flour, which is derived from coconut flesh and is completely grain-free and nut-free (coconut is a fruit, not a tree nut, though some people with tree nut allergies may also be sensitive to coconut—check with your doctor if you have concerns). There is no wheat flour, almond flour, or any other grain or nut flour in the recipe. Additionally, the mozzarella cheese, eggs, and zucchini are all gluten-free and nut-free. However, always check the labels on your specific brands of everything bagel seasoning and baking powder, as some may contain trace amounts of gluten or be processed in facilities that handle nuts. This recipe is a wonderful option for those following a gluten-free, nut-free, or grain-free lifestyle.
Share Your Version!
I absolutely love hearing from you—it’s the best part of running this little corner of the internet. If you make these low carb zucchini bagels, please leave a star rating and a comment below telling me how they turned out! Did you try one of the variations (the spicy Moroccan harissa bagels are a personal favorite)? Did your family eat them before you could even snap a photo? I want to know everything. Your feedback helps me create better recipes for you, and it helps other readers know what to expect.
Don’t forget to snap a photo of your bagel creations and share them on Instagram or Pinterest—tag @cheerychop so I can see them and feature my favorites! And if you have a question about the recipe that isn’t answered in the FAQ above, drop it in the comments and I’ll get back to you within 24 hours. From my NYC kitchen to yours — I hope this recipe brings as much warmth to your table as it does to mine. — Sara 🧡
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Zucchini Bagels (Low Carb, Keto)
Ingredients
- 3 cups zucchini, finely shredded
- 1½ cups low-moisture shredded mozzarella cheese
- ⅓ cup coconut flour
- 1 tsp baking powder
- 2 large eggs
- Everything bagel seasoning, for topping
Instructions
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