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Healthier Stuffed Breakfast Bagel Bombs

Have you tried my air fryer bagel recipe and thought, “man, that Matt guy is a genius?”

Okay, that’s not technically my recipe. A variation of the 2-ingredient dough has been floating around for years, so I can’t take full credit for it.

Protein Bagel Recipe

However, I can, and will, take the genius title for these breakfast bagel bombs.

Using a slightly altered version of the simple protein bagels, we’re going to make stuffed breakfast bagel bombs.

If you love breakfast sandwiches, this very well might become your favorite recipe of all time.

Bagel breakfast sandwiches are easily one of the best breakfasts on the planet, but they can be quite a mess. This recipe solves that issue!

Each of these breakfast bagel bombs is surprisingly filling and has only 300 calories and 23g of protein to keep you satisfied.

This recipe, and the associated nutrition facts, are based on the filling I used (I went with the classic bacon, egg, & cheese).

But the beauty of something like this is that you can fill it with whatever you want! Feel free to switch it up and use cream cheese, egg whites, avocado, you name it.

The world is your bagel.


How to make breakfast bagel bombs

If you want a quick walkthrough of this recipe, check out this web story!

My air fryer bagels are just self-rising flour (don’t worry if you only have all-purpose flour because that works too) and Greek yogurt, which is exactly how these bagel bombs start as well.

The difference here is in the ratio- we’re going to use slightly more Greek yogurt in order to shape the bagels easier. The bagel recipe is slightly denser because we just need to form rings, but in this case, we need to flatten the dough, so we’re going to use slightly extra yogurt!

Once we make the dough for the bagels, we’re going to split it up into 8 roughly equal-sized pieces.

Then we’re going to flatten them each out- these are going to be the top & bottom of each bagel bomb since we are making 4 total.

When you flatten out the dough, I like to make sure that one of the dough circles is slightly larger than the other.

Why is that? Because we’re going to add filling on top of one of the dough circles, then top with the other one, so the one on top needs to be slightly larger to be able to cover all of the fillings.

You can add any filling you’d like, but I stick with the classic American cheese, scrambled eggs, and bacon.

When it comes to the cheese, make sure you leave room around the edges! We need to be able to fully seal the entire breakfast bagel bomb, and we don’t want any cheese oozing out while it cooks.

Remember how we made one of the flattened dough circles slightly larger? This is why! We’re going to cover the filling and pinch down all the edges.

If you lay your dough over the top and find that it’s not large enough, don’t sweat it! Simply flatten it out more until it’s the right size you need.

Once we prep all 4 bagel bombs, we just need to add them to the air fryer, brush them with a light egg wash, and top with seasoning.

All we need to do is air fry at 350 degrees for 10 minutes, and these bagel bombs are ready to go!

These bagel bombs are made in the air fryer because it produces the best result. If you don’t have an air fryer, these work in the oven as well.

UPDATE: Thank you to Rebecca for providing what worked perfectly for her: 375 degrees for 12 minutes seems to be the way to go!

If you’re wondering what air fryer I recommend using… I don’t necessarily have a recommendation. I received the QVC brand air fryer as a gift (I’ll link it here for you) so it’s really all I know.

However, Amazon has a TON of different air fryers you can choose from, so you have plenty of options.


What to fill your bagel bombs with

I’ll level with you: I used to eat turkey bacon all the time in an effort to make recipes as healthy as possible, but I’ve come back around to using real-deal bacon.

I’m all for lower-calorie alternatives, but turkey bacon is just not the same.

I switched over to center-cut bacon, and I cannot recommend it enough.

In case you’re unfamiliar, center-cut bacon is still just regular pork bacon, but it’s trimmed of most of the fat. It still gets very crispy and delicious, but it’s lower in calories and fat than traditional bacon.

2 slices come in at just 50 calories and 4g of fat, which is not bad at all! Considering you do not need to compromise on taste, there’s no reason not to use center-cut bacon.

However, something I learned very recently is that bacon nutrition info shows you the nutrition for pan-fried bacon, not raw bacon. That means that it’s the nutritional info for AFTER you cook the bacon and drain the fat.

For a while, I was just cooking with the bacon grease left in the pan because it was only costing me 50 calories total. Turns out, that wasn’t true at all. The grease was likely adding 100s of extra calories, so be sure to actually drain your bacon grease.

What I like to do now is remove my bacon from the pan and drain the grease, leaving only a tiny bit of grease in the pan.

Yes, it is adding a few extra calories, but it’s minimal. I leave just enough in the pan to then cook my eggs in that for some extra flavor instead of using a nonstick spray. You certainly don’t have to do that, but the extra flavor is excellent.

I scrambled up some really basic eggs to add to my bagel bombs, and between you and me, I don’t even season them.

The saltiness from the bacon, along with the seasoning on top of the bagel bombs, was plenty for me. But you can spice these up however you want.

Bacon cooking tip: dice up your bacon before frying it in your pan.

You can absolutely pan-fry full strips of bacon, or use the microwave or air fryer, but I find it much easier to dice the bacon up and then cook it.

In the case of this recipe, I wanted to dice it up anyway, so it just made sense. When you dice the bacon prior to cooking it, you don’t have to mess with flipping each strip and getting splashed in the eye with scolding hot grease.

Instead, all you need to do is move them around in the pan a bit until they’re nice and crispy.


Some other creative filling ideas

Like I said, you’re not limited to a bacon, egg, and cheese. It’s the GOAT when it comes to breakfast sandwiches, but switch it up! If you want some ideas to get the juices flowing, here are a few:

Get wild with it, and please share your recreations with me on Instagram! I love seeing what you guys can come up with.

Breakfast Bagel Bombs

Stuffed Breakfast Bagel Bombs

Stuffed Breakfast Bagel Bombs

Yield: 4 Bagel Bombs
Prep Time: 15 minutes
Cook Time: 10 minutes
Total Time: 25 minutes

Simple 2-ingredient bagels loaded full of cheese, eggs, and bacon, and made in just 10 minutes in the air fryer! It's all the best parts of a bagel breakfast sandwich without any of the mess.


Bagel Ingredients

  • 180g (1.5 Cups) Self Rising Flour. You can also use the same amount of All Purpose Flour plus 2 teaspoons baking powder.
  • 200g Plain Nonfat Greek Yogurt
  • 1/4 tsp Salt (use 1/2 teaspoon if using AP flour)
  • 1 Egg for Egg Wash
  • Everything Bagel Seasoning

Filling Ingredients

  • 4 Eggs
  • 1 tbsp Milk of Choice
  • 4 Slices Fat Free American Cheese (or any cheese)
  • 4 Strips Center Cut Bacon


  1. In a large bowl, mix together all of your bagel ingredients except the seasoning and egg wash. Use a silicone spatula to mix it up until you have a dough. Don't be afraid to get in there with your hands to press everything together.
  2. Transfer the dough to a lightly floured surface, then separate the dough into 4 roughly equal sized balls. Break each ball in half, for a total of 8. It's okay if there are not all exactly the same size.
  3. Take 2 of the balls and use your palms to flatten them into circles (they don't have to be perfect circles). Flatten one of the them slightly more than the other so it is larger (this will be the top, so it needs to be able to cover the filling). Repeat until you have 4 pairs with one slightly larger circle for each. Set aside.
  4. If your dough is sticky during this process, you can put some flour on your hands to make it easier.
  5. Dice up 4 slices of bacon and add to a stovetop pan over medium heat. You can cook them as full slices using any method you like, but I find that dicing the bacon up first makes it significantly easier to get them crispy (with less mess). More them around in the pan occasionally until they're fully cooked, which should only take about 5 minutes.
  6. Once the bacon is done, you can remove it onto a plate lined with a paper towel to absorb the grease and pour the grease out of the pan into a container (you don't want to pour hot grease into a drain!), leaving a little bit in the pan to cook the eggs. You can cook the eggs in a different pan if you prefer, but I love the extra bacon flavor. Crack 4 eggs into a bowl with a splash of milk (roughly 1 tablespoon, but I don't measure it) and whisk together.
  7. Pour the eggs into the pan and use a spatula or wooden spoon to keep the eggs moving so they do not burn. They should take less than a minute to scramble in the hot pan. Pour the eggs out onto a plate when they're still slightly undercooked since they're going into the air fryer.
  8. Now it's time to assemble the bagel bombs. Take your SMALLER circle you made, and add a slice of cheese (I cut the corners off to make it fit), some of your eggs, and some bacon. Sriracha is definitely recommended as well! Drape your larger circle over the top to make sure it covers everything- if not, simply flatten it out some more to stretch it. Cover the filling, then pinch all of the edges to close it up. Repeat for all 4.
  9. Add your bagel bombs to the air fryer. Whisk up one egg in a bowl and brush the tops of each with the egg- this helps with the browning, and also to allow the seasoning to stick. Top each with your everything bagel seasoning or any seasoning of your choice, then air fry at 350 degrees F for 10 minutes.
  10. Let cool for a few minutes, then enjoy!


If you do not have an air fryer, reader Rebecca shared that you can make these in the oven at 375 degrees for 12 minutes for a perfect result.

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Nutrition Information
Yield 4 Serving Size 1 Bagel Bomb
Amount Per Serving Calories 310Total Fat 7gCarbohydrates 38gFiber 1.5gSugar 2.5gProtein 23g

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Wednesday 13th of December 2023

There’s a store near me that sells a beef, Emmental and pickle pretzel roll. I would put a veg twist and use Seitan “pulled beef” Emmental or any other creamy mild cheese and pickle it would be so good


Monday 18th of July 2022

I just made minis, one with goat cheese, caramelized onions, and mushrooms, and the other with salmon, cream cheese, and onion. My friends are gonna flip.


Wednesday 15th of September 2021

Curious if an almond flour would work for this?


Sunday 3rd of April 2022

@Jess, unfortunately it doesn't work because almond flour lacks structure without gluten, so it's very loose & sticky. I found another recipe online that you may be able to use to turn them into stuffed bagels:


Sunday 3rd of April 2022

@Martha, I have the same question!!


Thursday 17th of June 2021

I just made these with chicken, pizza blend cheese, banana pepper, cherry tomato, and pasta sauce! So good!!! Thanks for the recipe!


Thursday 25th of March 2021

These are an absolute must try! They are on regular rotation in my house, every Sunday we have them for brunch. Don't be scared to mix up the fillers for something that better fits your taste or macros, we do bacon, sausage, veggies, just cheese. The possibilities are endless.

About Matt Rosenman

With over 15 years of experience in health and fitness, Matt Rosenman is the expert voice behind Matt’s philosophy is simple: no foods are off-limits, and a healthy lifestyle shouldn't be complicated or restrictive. As a former certified personal trainer with a bachelor’s degree in Health Behavioral Sciences, Matt brings well-rounded expertise to his blog. From revamping classic recipes with a nutritious twist to breaking down fast food menus, his goal is make healthy living less confusing for everyone. Featured in major publications and with a strong following on social media, Matt is committed to making “healthy” uncomplicated—no matter where you are in your health journey. Join Matt on his mission to simplify health without sacrificing flavor. Learn More

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