High Protein Stuffed Bagel Bites

I love bagels. Unfortunately I haven’t found a good bagel that is low carb and high protein. Luckily, there are some decent recipes online, but they always lack the high protein part. These high protein stuffed bagel bites are a delicious and healthy option!

Half eaten bagel bite on a plate with cream cheese in the middle

Bagels are my weakness. I remember the first one I ever ate. It was in NYC, and it was an egg bagel. I hated it. I thought it was so gross. The next time I had a bagel, it was like my taste buds had finally gotten a clue. Unfortunately, bagels aren’t the best option in a post-Bariatric meal plan. 

How I came across this recipe

I have a somewhat newfound love for Skinnytaste. I’ve visited her site multiple times over the years, and I’ve used a lot of her recipes. I found a recipe for stuffed bagels bites on her site, and then again in one of her books.  Honestly, I love her recipe. And if I wasn’t trying to get more protein into my diet, I wouldn’t change anything about her recipe. 

But I am, so I did. 

Enter, unflavored protein powder. 

How to make High Protein Bagel Bites

Divide a block of Neufchâtel cream cheese into 12 equal pieces, transfer to the fridge to garden the blocks. This makes it much easier to work with. I kept my cream cheese plain,  but adding chives or any other additives would probably be delicious. 

12 cut chunks of cream cheese on cutting board

In a bowl on your trusty kitchen scale, weigh out 1 oz of unflavored protein powder. I prefer Genepro, because in 7.2 grams, there are 30 grams of protein. Since 1 ounce equals about 28 grams, that’s about 120 grams of protein. Across 12 bagel bites….well, I’ll let you do the math. 

Add flour, along with baking powder and salt. Mix this together well, and then add in your Greek Yogurt. My favorite is Fage 0, but I’ve tried Chobani and that works well too. I think any Greek Yogurt will work well here. 

Using a spatula, mix well (1). This will take a bit of muscle to bring it all together, but once it’s resembling a dough, dump onto a floured surface and knead it to bring it all together. 

Divide the dough into 12 equal balls (2). I actually used my kitchen scale to help with this task, but if you’d rather do it by eye, that works, too. Flatten each ball, place a square of cream cheese in the middle, and fold over the dough to make a solid ball (3). I found that keeping the middle thicker than the ends helps to not make what becomes the top too thin. 

Bagel mixture in bowl, 12 bagel balls, flattened with cream cheese, 12 assembled balls on baking sheet

Place the balls on a baking sheet lined with parchment paper (4). Coat lightly with a beaten egg and add the toppings of your choice. I like using sesame seeds and everything bagel topping. 

assembled bagel bites on baking tray with toppings

Bake at 375* for about 25 minutes until golden brown. Remove from oven and let cool to room temperature on the baking sheet. Once cooled, transfer to the freezer to flash freeze. 30-60. Instead is fine. Once frozen transfer to zip bags and store in the freezer. 

Baked bagel bites on baking sheet with toppings

Any morning that you’re in the mood for a bagel, place a bite on a paper towel and microwave at 30 second intervals for about 1.5-2 minutes. The middles will be very hot, so be careful! But enjoy. These are so amazing!!


There are so many options for variety here. You can put some additions into your cream cheese. You can make a chive cream cheese or a veggie cream cheese, or any flavor you want. Depending on your filling, you can change up the toppings. Plain, a bit of salt, sesame seeds, everything bagel seasoning, or poppy seeds – they are all options!

Bagel Bite with sesame seeds on top on a white plate
Half eaten bagel bite on a plate with cream cheese in the middle

High Protein Stuffed Bagel Bites

I love bagels but it's hard to find a low carb/high protein option. These high protein stuffed bagel bites are a delicious and healthy option!
Prep Time 20 mins
Cook Time 25 mins
Course Breakfast
Servings 12 Bagel Bites
Calories 167 kcal


  • 1 oz Unflavored Protein Powder (I used Genepro)
  • 9 oz All Purpose Flour
  • 4 tsp Baking Powder
  • tsp Kosher Salt
  • 2 cups Fage 0% (about 16 ounces)
  • 8 oz Neufchâtel Cream Cheese
  • 1 egg beaten
  • 1 Tbsp Everything Bagel Seasoning or your topping of choice


  • Divide the block of cream cheese into 12 equal sized chunks. Place them in the freezer while working on the bagel dough steps.
  • Using a kitchen scale, measure 1 ounce of protein powder and 9 ounces of flour. Add in the baking powder and kosher salt and whisk together.
  • Add the Greek Yogurt and mix together well. Once it is mostly together, dump onto a floured surface and knead until it is fully mixed together.
  • Separate into 12 equal sized balls. Flatten each ball and place one frozen square of cream cheese into the center of each. Fold over the excess dough to cover all of the cream cheese
  • Place the balls onto a baking sheet lined with parchment paper. Lightly coat each of the balls with the egg wash (you will use very little of it) and then top with your topping of choice.
  • Bake at 375* for 25 minutes, until golden brown. Allow to cool on the baking pan for at least 30 minutes before eating.


  • You can omit the protein powder, but it will significantly reduce the amount of protein in each bagel bite.  I chose to use unflavored, but you could always use a flavored powder.
  • You can mix things into the dough itself or you can mix ingredients into the cream cheese if you want a flavored stuffed bagel bite.
  • There are no limits to the type of toppings you can use!  
  • To freeze, place in the freezer on the baking sheet to initially freeze the bagel bites. After about an hour, once the stuffed bagel balls are frozen, move them to a zip-lock freezer bag. To reheat, microwave for about 1½ minutes, in 30 second intervals.
Nutrition Facts:  Servings 12.0 * calories 167 * Total Fat 4 g * Saturated Fat 3 g * Monounsaturated Fat 0 g * Polyunsaturated Fat 0 g * Trans Fat 0 g * Cholesterol 21 mg * Sodium 559 mg * Potassium 59 mg * Total Carbohydrate 18 g * Dietary Fiber 1 g * Sugars 2 g * Protein 18 g
*All nutritional information is based on third-party calculations and should be considered estimates. Actual nutritional content will vary with brands used, measuring methods, portion sizes, and more.*
Post Disclaimer

I am not a doctor or a dietitian.  The information I provide is based on my personal experience.  Any recommendations I may make about nutrition, supplements, lifestyle, or fitness, or information provided to you on this website should be discussed between you and your doctor.  The information on this site does not take the place of professional medical advice.

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