Best High Protein Low Carb Keto Cottage Cheese Bagels

The texture of these high protein keto cottage cheese bagels is truly like a chewy high carb bagel from your past! But these have just 4 total grams of carbs and  an amazing 18 grams of protein! Super quick and easy, no whipping egg whites needed!

Keto Cottage Cheese Bagels

Ever found yourself craving a traditional bagel with cream cheese, but wanting to keep it keto-friendly and protein-packed? Well, you’re in luck because today we’re diving into my easy bagel recipe that hits those marks with a twist—cottage cheese bagels. 

These bad boys are low carb but still super satisfying, and they bring a nice bounce of protein to the table. Plus, they’re surprisingly easy to whip up, so whether you’re fresh into keto or just here for a tasty snack, you’re gonna want to stick around.

3-Ingredient Cottage Cheese Bagels

The cottage cheese trend is hot right now everywhere and for good reason, everyone is looking to increase their protein intake. 

Most of the 3-ingredient cottage cheese bagels I’ve seen on the internet usually contain dry ingredients like self-rising flour, all purpose flour or even gluten-free flour but sure, all using 3 simple ingredients making them high protein bagels, but none of them are keto bagels. 

I did see one influencer on tiktok- make keto high-protein bagels recipe but it included almost 2 cups of almond flour which is something I don’t want to use since my youngest son has a tree nut and peanut allergy and it doesn’t agree with me either. 

My goal for this keto bagel recipe was to get in a high amount of grams of protein to create chewy bagels with the right consistency for that bagel shape I wanted and still fit into my midlife macro method™ that has more moderate fat, instead of high fat typically seen in keto recipes. 

I adapted from my coconut flour regular bagels that use 12 eggs and make 12 bagels with a decent amount of extra protein from all the eggs and the fat amount is moderate too, but I wanted to reduce the amount of eggs for a fluffier texture and increase the protein intake even more. 

My newest version for keto cottage cheese bagels recipe has 18 grams of protein which makes me super happy! You can find all the nutritional information at the bottom of this page on the printable recipe card. 

What Makes This Recipe Great

Super high in protein.
Thanks to the cottage cheese and whey protein powder, these bagels pack a solid protein punch that keeps you full and energized without the carbs knocking you out of ketosis. It’s like giving your breakfast a power-up.

Low carb and keto-friendly.
Say goodbye to heavy bread guilt. These bagels ditch the usual flour and embrace ingredients that fit perfectly into keto diet and low carb lifestyles, making it simple to enjoy your favorites without breaking your macros.

MMM™ Approved. If you’re following my Midlife Macro Method™, you can enjoy these on a deficit day!

Light, fluffy, and versatile.
Unlike some dense keto bread alternatives, these bagels have a great texture—just the right fluffiness with a slight chew. Plus, you can enjoy them with a savory seasoning mix or sweet toppings like keto cinnamon sugar and still keep it keto.

Simple Ingredients and Substitutions

Cottage Cheese

This is the star of the show. Cottage cheese provides moisture, protein, and a slight tang that really lifts the bagels. If you want to mix it up, ricotta cheese can be a decent substitute but expect a slightly different texture or greek yogurt, plain. 

Eggs and egg whites

Eggs act as the binder and help the bagels rise a bit, giving that nice structure. If you’re allergic or avoiding eggs, flax or chia egg substitutes work, but the texture might change a bit. I do not recommend swapping either of these ingredients.

Coconut Flour

Coconut flour is super absorbent — 2 tbsp goes a long way. If you swap it:

• Almond flour – Use 3× the amount (so 6 tbsp / 42g for this recipe). Lower absorbency = softer, slightly more crumbly bagel, and carbs will increase slightly.
• Oat fiber – Use 1:1 swap (14g). Zero net carbs, keeps carbs very low, but gives a drier crumb — add 1–2 tbsp extra cottage cheese for moisture.
• Ground sunflower seed flour – Use 3× the amount like almond flour. Flavor is mild; watch for greenish tint if using baking soda (harmless reaction).

Whey Protein Powder Substitutes

Best Choices for Similar Texture & Rise

• Whey/Casein Blend – 1:1 swap. Casein gives more structure and chew, often producing a slightly more bread-like crumb.
• Egg White Protein Powder – 1:1 swap. Very high protein, low fat/carb, and gives great lift, but can be a little drier — increase cottage cheese to 1 cup which provides more moisture that is needed.
• Beef Protein Isolate – 1:1 swap. Mild flavor if unflavored; denser crumb than whey but still works well in high-protein baking.

Flavor Boosters

Add Garlic Powder or Onion Powder
A pinch of garlic or onion powder mixed into the dough delivers a subtle savory kick that makes these bagels taste even more like classic bakery goods.

Mix in Chopped Jalapeños
For a little heat, toss some finely chopped jalapeños in the mix. It’s a surprise punch of flavor that makes the bagels stand out.

Incorporate Fresh Herbs
Fresh chopped parsley, chives, or dill folded into the dough brings brightness and freshness you don’t expect from a bagel.

Freezing & Storing Leftovers

At Room Temperature

• 1 day max in an airtight container or wrapped — after that, they can get overly moist and risk bacterial growth due to the dairy/eggs.

In the Fridge

• Up to 5 days in an airtight container or zip-top bag.
• Place a paper towel in the container to absorb excess moisture so the tops don’t get sticky.

In the Freezer

• Up to 3 months.
• Wrap each bagel individually in plastic wrap, then place in a freezer-safe bag.
• Thaw at room temp or reheat straight from frozen in the oven/air fryer at 300°F (150°C) for 8–10 minutes.

Tip: Because these are high in whey isolate, reheating briefly in the oven or toaster oven is better than the microwave, which can make them rubbery.

Can I use full-fat vs low-fat cottage cheese?

Yes, full-fat cottage cheese can be used. I opted for low fat and lactose free using my homemade 2% lactose free cottage cheese recipe but it fits better into my Midlife Macro Method™. You could also swap with fat-free cottage cheese but it may change the texture. 

Can I swap cottage cheese with Greek yogurt?

Yes you could probably swap the cottage cheese to make Greek yogurt bagels though I haven’t tested this myself. 

Can I replace the coconut flour with almond flour?

It is difficult to say whether you will get the same best results in texture as I did if you replace coconut flour with a few tablespoons of almond flour since they are not an even swap. 1/4 cup coconut flour is about equal to 1 cup almond flour. If you do test it out please come back and let me know in the comments below. 

Can I form the bagel dough in thick ropes and placed on a parchment paper lined sheet pan?

The whipped cottage cheese and all ingredients are added to a food processor because it is not a sticky dough. The dough forms but it is not moldable, it is still pourable and needs a silicone standard size donut pan.

Easy Protein Bagels

Giving these cottage cheese bagels a try totally changed my breakfast game. They’re not only easy on the carbs but also pack enough protein to fuel your day in a way that feels good, not like a struggle. And the texture? 

Kinda surprising in a good way—fluffy with that nice bagel chew but without the heaviness. So next time you’re craving a bagel but aiming to stick to keto, these will be your go-to, no biggie. Grab your ingredients and let’s get baking.

More High Protein Cottage Cheese Recipes

Keto Cottage Cheese Pancakes

Keto Cottage Cheese Muffins

Keto Cottage Cheese Chicken Crust Pizza

Keto Cottage Cheese Waffles

Keto Cottage Cheese Cloud Bread

High Protein Keto Cottage Cheese Homemade Bagels