Chewy Keto Cheese Bagels with Everything Topping

Written by Sarah Gardner

These chewy keto cheese bagels are the perfect low‑carb breakfast or snack for anyone craving that satisfying bagel texture without the carbs. Made with almond flour and Mozzarella cheese, they pack a punch of flavor with an everything topping blend—poppy, sesame, garlic, and onion. They're easy to prepare, gluten‑free, and perfect if you’re in the mood for a healthy bagel breakfast or a midday nibble. Whether you’re new to keto or a seasoned pro, this recipe hits the sweet spot.

Chewy Keto Cheese Bagels

Prep Time 15 minutes
Cook Time 20 minutes
Total Time 35 minutes
Course Breakfast, Snack
Cuisine American
Servings 6 bagels

Equipment

  • Large microwave-safe bowl (alternatively use double boiler)
  • Rubber spatula
  • Stand mixer with paddle attachment or mixing bowl and hand mixer
  • Cooling rack
  • Parchment-lined baking tray
  • 1 cup measuring cup (for shaping bagels)
  • Optional: Kitchen scale (for more precise bagel amping)

Ingredients
  

Dry & Binders

  • cups blanched almond flour use in keto bagels almond flour substitutions
  • ¼ cup coconut flour optional for structure
  • 1 tbsp baking powder
  • 1 tsp garlic powder
  • ½ tsp salt

Cheese & Egg Base

  • cups shredded Mozzarella chees
  • ¾ cup cream cheese softened
  • 2 large eggs see FAQs for egg bagel recipe guidance
  • 1 tsp apple cider vinegar

Topping – Everything Bagel Blend

  • 1 tbsp black sesame seeds
  • 1 tbsp white sesame seeds
  • 1 tbsp poppy seeds
  • 1 tsp dried minced onion
  • 1 tsp dried minced garlic

Optional: pinch of coarse sea salt

Instructions
 

Preheat & Prep

  1. Preheat oven to 200 °C (400 °F). Line a baking tray with parchment paper.

Mix Dry Ingredients

  1. In bowl, whisk together almond flour, coconut flour (if using), baking powder, garlic powder, and salt. This forms your low carb bagels foundation.

Melt Cheeses

  1. Combine shredded Mozzarella and cream cheese in microwave-safe bowl. Microwave in 30-second intervals, stirring between each, until fully melted and smooth. Alternatively, melt in a double boiler over simmering water.

Combine & Knead

  1. Add the melted cheese mixture to the dry ingredients. Add eggs and vinegar. Use stand mixer on low with paddle attachment, or fold and knead gently by hand until a sticky but moldable dough forms. This is a classic chewy low carb keto bagels recipe dough.

Shape Bagels

  1. Generously coat hands with water (to prevent sticking). Divide dough into 6 equal parts. Roll each into ropes, form bagel shape by connecting ends. Alternatively, use a 1 cup measuring cup to shape even rounds with a central hole.

Add Topping

  1. Brush bagels lightly with water or beaten egg. Dip the tops into the everything mixture to adhere.

Bake

  1. Place bagels on parchment tray and bake for 18–20 minutes until golden brown and set. Turn halfway for even crispiness.

Cool

  1. Let bagels cool on a rack at least 10 minutes before slicing. Cooling ensures they maintain their chewy texture.

Pairings

  • Savory Fillings: Classic cream cheese and smoked salmon, herb‑infused goat cheese, or sliced avocado with tomato and arugula.
  • Breakfast Idea: Halved, toasted lightly, topped with scrambled egg, bacon bits, and a drizzle of hot sauce.
  • Deli‑Style Sandwich: Grilled chicken breast, spinach, sliced cucumber, Dijon mustard, or mayo in a low carb bagels sandwich.
  • Soups & Salads: Serve alongside creamy tomato basil soup or roasted root veggie salad for a hearty, balanced lunch.
  • Desayuno Keto Variation: Top bagel halves with refried black beans, queso fresco, a fried egg, and cilantro for a Mexican-inspired morning burst.

FAQs

1. Can I use just eggs without cheese for a 2-ingredient keto bagels version?

Not quite—egg bagel recipe using only eggs and cheese is common, but without cheese, the bagel won’t hold shape. Two-ingredient recipes refer to cheese + egg, so you could skip almond flour entirely for a super simple cheese‑egg dough (see inspirations in keto bagels 2 ingredients).

2. Is there a best keto bagel recipe for a chewier texture?

Yes, adding cream cheese and using Mozzarella yields chewiness. Optionally chilling dough before baking helps firm them up. It’s one of the best chewy low carb keto bagels recipes you’ll find.

3. Can I swap almond flour with coconut flour?

You can, but coconut flour absorbs more liquid. For low carb bagels with almond flour replacement, you’d use about ¼ cup coconut flour per 1½ cups almond flour, and add another egg. Expect denser texture.

4. What meat fillings work best?

Use lean, thinly sliced meats like turkey or chicken breast. Thigh meat works too but may add extra fat. Best lean balance comes from breast. For a warming twist, grilled chicken topped with pesto and roasted red onions is delightful.

5. Are these bagels safe for gluten‑free diets?

Yes! These are inherently gluten free thanks to almond flour and no wheat. It’s a gluten free bagel recipe that doesn’t compromise taste or texture.

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