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But First We Brunch » Recipes » Breads and muffins

3-Ingredient Stuffed Bagel Bites

Published: May 27, 2024 by Cynthia Christensen · This post may contain affiliate links · 4 Comments

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4.50 from 2 votes
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These new 3-Ingredient Stuffed Bagel Bites are going to get me run out of New Jersey! Around here it's a residency requirement to love bagels, and we also run on Dunkins, but since I've stopped buying donut shop stuffed bagel minis, and making them at home, I might be in trouble!

A cream cheese stuffed bagel bite with a bite taken out.

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If you love Dunkin Donuts cream cheese filled bagel minis, you are going to lose your mind over my 3-Ingredient Stuffed Bagel Bites. Made with a simple dough, and full of luscious cream cheese, they require no yeast, no boiling, and can be in your mouth in less than an hour, for a fraction of the cost!

We start with a version of the two ingredient dough that I used to make my quick and easy english muffins, my chewy bagels, and my yogurt flatbread. Then you fill them with balls of cream cheese, add toppings if that's the vibe, and bake them to a golden brown.

Jump to:
  • ❤️ What you'll love about these bite-sized cream cheese filled bagels
  • Ingredients
  • NOTE ABOUT GREEK YOGURT
  • What is self-rising flour?
  • Making your own self-rising flour
  • Substitutions
  • Variations
  • Instructions
  • Serving suggestions
  • Expert tip
  • Recipe FAQs
  • Minimal ingredient recipes
  • 📖 Recipe
  • 💬 Comments

❤️ What you'll love about these bite-sized cream cheese filled bagels

  • Simple - With just a few ingredients, and no need to wait for yeast to do its job, this is the perfect recipe for busy mornings and novice bakers.
  • Great bagel texture - The combo of self rising flour and Greek yogurt creates a dough that bakes up soft and chewy, just like your favorite bagels.
  • Customizable - You can leave these plain, or use your favorite bagel toppings; everything bagel seasoning, sesame seeds, poppy seeds, and pretzel or flaky salt are my favorites! 
  • Portable - No more balancing a cream cheese bagel on your lap while driving. This copycat bantam bagels recipe is perfect for an easy breakfast, to pack for lunch, or for on-the-go snacking. 
  • Air fryer friendly - Set your air fryer to 330°F. Spray the inside of your air fryer with nonstick spray and place a dough ball, seam side down, in basket. Air fry for 10 to 12 minutes, or until golden brown. Remove bagel bites from the basket, and cool for about 10 minutes before serving.

Ingredients

SO much to remember to pick up at the mega market. Need to borrow a pen so you can write it all down?

Labeled image of ingredients to make 3 ingredient bagel bites.

See recipe card below for quantities.

NOTE ABOUT GREEK YOGURT

It’s very important that you use a thick Greek yogurt for this recipe. I've used Stonyfield and Cabot, as well as my local store brand, and they all work well. If you use plain (non-Greek) yogurt or your yogurt is runny or has excess liquid in it, it will probably make the dough too sticky, so be sure to allow any visible liquid drain off before measuring out your yogurt. 

It's always easier to start out with a drier dough and add more liquid to hydrate it than the other way around. If your dough looks dry, add more yogurt, one tablespoon at a time, up to ¼ cup, until it comes together as shown in the instructions below. 

If you don't have Greek yogurt, you can make high-protein bagels with cottage cheese. I know some recipe developers have you blend the cottage cheese to break up the curds, but I tested this recipe with blended curds and natural curds and found they worked equally well.

What is self-rising flour?

Although similar to all-purpose flour, self-rising flour already contains baking powder and salt, eliminating the need to add either of these ingredients to your recipes. This means you can make light and fluffy muffins, pancakes, waffles, and even old fashioned biscuits quickly and easily.

Making your own self-rising flour

Self-rising flour is quite common in the American South, where we use it to make cornbread and biscuits, and just about everything else. But apparently not everyone keeps self-rising flour in their pantry.

If you don't have self-rising flour, you can make your own. For every cup of self-rising flour that you need, combine 1 cup of all-purpose flour (120 grams) and add 1 ½ teaspoons of baking powder and ¼ teaspoon of kosher salt. If you don't have kosher salt, you can use a tiny pinch of table salt. 

For a more classic bagel chew, you can also make your own self rising bread flour, using the same measurements.

Substitutions

Perfect just the way they are, sometimes you have a dietary restrictions that call for a pivot. Here's a few you can make this recipe work for you:

  • Gluten-free - Try using a one-to-one gluten-free flour in place of the self rising flour, and adding baking powder and salt to it, as described above.
  • Dairy free - To make dairy free, and vegan, stuffed bagel bites, use thick vegan yogurt in the dough and fill them with vegan cream cheese. Also, skip the egg wash and brush your bagel bites with plant based milk, aquafaba, olive oil , or even spritz lightly with nonstick cooking spray before adding any toppings.

Variations

Play with your food. All the cool kids are doing it.

  • Flavored - There are a few flavored cream cheeses out there on the market, from fruit flavored, to herb filled. Just make sure to use brick cream cheese, not the kind in a tub, which melts away during baking.
  • Sweets for your sweeties - For a sweet version, add some fruit jam or cinnamon sugar to your cream cheese and sprinkle with a little sugar before baking.
  • Jalapeno cheddar - Add cheddar and some chopped pickled jalapenos to your cream cheese filling.
  • Pizza - Roll a ball of mozzarella cheese in marinara sauce and freeze. When ready to make your bagel bites, wrap a small piece of pepperoni and a frozen mozzarella ball in your chewy bagel dough.
  • Pretzel me! - I've unlocked the secrets to making bagels with a total Auntie Anne's vibe! No need to drive to the mall, make these into pretzel bagels with a cream cheese filling!

Don't feel like stuffing a bagel just for yourself Make one classic bagel - just for yourself and schmear all the cream cheese your heart desires. My Bagel for One (or two) makes one big bagel for when you want to treat yourself.

Instructions

Making these cream cheese stuffed bagels is easier than you can imagine:

Twelve one tablespoon balls of cream cheese on a parchment lined sheet pan.

Step 1: Use a tablespoon or tablespoon scoop, to place dollops of cream cheese onto a baking sheet  lined with parchment paper or aluminum foil. Place into the freezer to harden while you make your dough.

Mixing greek yogurt into self rising flour.

Step 2: In a large mixing bowl, combine self rising flour with Greek yogurt until you have a shaggy, clumpy dough. If the dough seems too dry, add more yogurt, 1 tablespoon at a time, up to ¼ cup, until it comes together.

Rough shaggy 2 ingredient dough before kneading.

Step 3: Dump the dough onto a lightly floured surface.

Kneading 2 ingredient dough into a smooth dough.

Step 4: Gather together into a rough ball and knead the dough for 3 to 4 minutes, or until you have a soft dough with a smooth surface. Dust the counter, the top of the dough, or the palm of your hands with more flour if the dough sticks.

Rolling bagel dough into a large ball.

Step 5: When the dough forms, it should be smooth and only a little bit sticky. Shape into a ball and cover with plastic wrap. Let rest for 15 minutes, while you preheat the oven to 375°F.

Pinching dough together on the bottom to form a ball.

Step 6: Divide into 12 equal portions (about 70 to 75 grams each).

Rolling bagel dough into a ball.

Step 7: Shape each piece into a ball.

Pressing a piece of frozen cream cheese onto bagel dough.

Step 8: Flatten a piece of the dough and place a ball of frozen cream cheese into the center.

Pinching the dough around frozen cream cheese to make bagel bites.

Step 9: Bring the edges of the dough over the cream cheese ball and pinch closed. Roll on the counter, seam side down, to help seal the dough closed completely.

Brushing an egg wash on unbaked stuffed bagel bites.

Step 10: Make an egg wash with a large egg whisked with 1 tablespoon of water, some milk, or mix more greek yogurt with a bit of water to make a milk consistency. Brush the top of each bagel with your chosen wash.

Sprinkling everything bagel seasoning on an unbaked bagel bite.

Step 11: Sprinkle with your choice of toppings, if desired.

Unbaked cream cheese stuffed bagel bites on a sheet of parchment paper.

Step 12: Place all the stuffed bagels on a parchment lined sheet pan and bake at 375°F for 20 to 25 minutes, or until fully browned.

Cream cheese stuffed bagel bites on a sheet of parchment paper.

Hint: Check your bagels at 20 minutes, and keep checking every minute or so to catch if any of your bagel bites start to leak. Pull out of the oven and let cool completely. The dough will still be baking from residual heat, so avoid the temptation to bite into one immediately. Plus, that cream cheese is HOT! I just saved your tongue and the roof of your mouth.

Serving suggestions

  • Pack them in your kids' lunch box for school, day camp, or a play date.
  • Make a couple of batches and serve them as part of a brunch board along with some crispy waffles, fluffy pancakes, blueberry muffins, and all the fresh fruit!
  • Serve them in place of toast or biscuits and alongside creamy scrambled eggs and crispy bacon strips!
Eggs and bacon with stuffed bagel bites.

Expert tip

You might be tempted to skip the frozen cream cheese bit. You might even be tempted to just use a scoop of whipped cream cheese, you know, the kind in the tub. Don't do it!

Whether you are making yeast based bagel dough, or two ingredient dough, if you bake them long enough, the cream cheese will start to melt into the dough or bagels will try to spring a leak. Using frozen cream cheese gives you a head start on keeping the cheese intact and inside, where it belongs.

If you feel you might be pressed for time in the morning, you can freeze your cream cheese balls ahead of time. You can even make your dough ahead, wrap tightly in plastic wrap, and refrigerate for up to 3 days, or freeze for 3 months. Thaw overnight in the refrigerator.

Cream cheese stuffed bagel bites on a sheet of parchment paper.

Recipe FAQs

Can I make the dough in a stand mixer?

Yes you can. I like to use the paddle attachment and just mix until the dough comes together. You can also use the dogh attachment if you like, mixing until the dough just comes together.

How do I store leftover stuffed bagels?

Place into a airtight container, or freezer bag for up to 3 days or freeze for up to a month.

How do I reheat/serve leftover bagel bombs?

Allow frozen bagel bites to thaw at room temperature, or pack in your lunch box to keep things cold as they thaw. Eat at room temperature or reheat by toasting or placing in a 350°F oven for 5 minutes. I don't recommend microwaving them as it will dry out the bagel and make it unpleasantly chewy.

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Cynthia from But First We Brunch writing down a brunch recipe.

Did you try this recipe?
Leave a comment with a ⭐️ rating below to tell me all about it, and don't forget to tag me on Instagram!
I appreciate you!
-Cynthia

📖 Recipe

The author's hand holding a cream cheese stuffed bagel bite with a bite taken out.

3-Ingredient Stuffed Bagel Bites

These new 3-Ingredient Stuffed Bagel Bites are going to get me run out of New Jersey. Around here it's a residency requirement to love bagels, and we also run on Dunkins, but since I've stopped buying donut shop stuffed bagel minis, and making them at home, I think I'm in trouble!
4.50 from 2 votes
Author: Cynthia Christensen
Print Recipe Pin Recipe
Prep Time 20 minutes mins
Cook Time 25 minutes mins
Total Time 45 minutes mins
Course Breakfast, Brunch, lunch, Snack
Cuisine American
Servings 12 bagel bites
Calories 205 kcal

Equipment

  • Large silicone spatula
  • Parchment paper
  • Small sheet pan
  • Large sheet pan
Prevent your screen from going dark

Ingredients
 

  • 12 tablespoons (174 g) cream cheese brick style - not whipped
  • 3 cups (360 g) self rising flour
  • 2 cups (500 g) Greek yogurt

Optional toppings

  • 1 large egg
  • 2 tablespoons sesame seeds
  • 2 tablespoons poppy seeds
  • 2 tablespoons everything bagel seasoning

Instructions

  • Use a tablespoon, or small cookie scoop, to place dollops of cream cheese onto a parchment paper, or foil lined sheet pan. Place into the freezer to harden while you make your dough.
  • In a large bowl combine self rising flour with Greek yogurt until you have a shaggy, clumpy dough. If the dough seems too dry, add more yogurt, one tablespoon at a time, up to ¼ cup, until it comes together.
  • Dump the dough onto a lightly floured counter. Gather together into a rough ball and knead the dough for 3 to 4 minutes, or until you have a soft dough with a smooth surface. Dust the counter with more flour if the dough sticks (see pictures in post, above).
  • When done, the dough should be smooth and only a little bit sticky. Shape into a ball and cover with plastic wrap. Let rest for 15 minutes, while you preheat the oven to 375°F.
  • Divide into 12 equal pieces (about 70 to 75 grams each). Shape each piece into a ball.
  • Flatten a piece of the dough and place a piece of frozen cream cheese into the center.
  • Bring all of the edges over the cream cheese ball and pinch closed. Roll on the counter, seam side down, to help seal the dough closed completely.
  • Make an egg wash with a large egg whisked with 1 tablespoon of water, some milk, or mix more greek yogurt with a bit of water to make a milk consistency. Brush the top of each bagel with your chosen wash. Sprinkle with your choice of topping.
  • Bake at 375°F for 20 to 25 minutes, or until fluffy and fully browned. Check at 20 minutes, and keep checking every minute or so to catch if any of your bagel bites start to leak. Pull out of the oven and let cool.

Save This Recipe! 💌

I'll email this recipe to you, so you can come back to it later, plus you'll get great new recipes from me every week!

Notes

Yogurt replacement: Thick Greek yogurt has the needed consistency to make the dough as intended in this recipe. In a pinch, you can use sour cream or cottage cheese (you can blend it smooth, but not required). Plain yogurt is too thin and adjustments would need to be made with the flour content. See substitutions section in blog post for vegan options.
Self-rising flour: You can make your own self-rising flour by adding 1 ½ teaspoons of baking powder and ¼ teaspoon of kosher salt to each cup of all-purpose flour.
Storage & reheating: Store cooled stuffed bagel minis in a zip top bag for up to 3 days on the counter. Reheat by toasting or placing in a 350°F oven for 5 minutes.
Freezing: To store bagel bites in the freezer for up to 1 month, freeze until solid on a sheet pan and then place in a zip top bag. Place directly into lunch boxes to keep things cold as they defrost or defrost on the counter at room temperature for half an hour before eating or baking to reheat.
Calories: 205kcal | Carbohydrates: 25g | Protein: 20g | Fat: 7g | Saturated Fat: 3g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 2g | Trans Fat: 0.003g | Cholesterol: 32mg | Sodium: 196mg | Potassium: 120mg | Fiber: 1g | Sugar: 2g | Vitamin A: 219IU | Vitamin C: 0.01mg | Calcium: 93mg | Iron: 1mg

The nutritional and caloric information shown is an estimate provided by an online nutrition calculator. It does not assert or suggest that readers should or should not count calories, and should not be considered a substitute for a professional nutritionist’s or doctor’s counseling.

Tried this recipe?I would love for you to leave a comment!

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    4.50 from 2 votes

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  1. Meghan P says

    March 24, 2025 at 12:16 pm

    5 stars
    While baking them my whole house smells like a bagel shop! I rolled the frozen cream cheese in everything but the bagel seasoning before putting it in the dough. Then rolled the seasoning on the outside as well. Definitely will be making these again! Super easy to make and my daughter can’t get enough of them!

    Reply
    • Cynthia Christensen says

      March 24, 2025 at 12:31 pm

      What a great idea!

      Reply
  2. Not Bad says

    December 22, 2024 at 11:59 pm

    4 stars
    My first time trying a bagel of its kind (yogurt based...I usually do traditional). I was pleasantly surprised. It's thick like a bagel, more chewy than fluffy (as many recipes I've come across seemed to describe yogurt based bagels as). I used a mixer, so maybe it was too rough on the dough, because I kept having to add flour, like a cup...the dough kept eating the flour but remaining sticky. finally I just added flour to each ball as I rolled them. I made my own self rising flour per the guidelines given. Overall 4 for a good recipe added pictures for guidance and a good experience trying a. new recipe. Thank you!

    Reply
    • Cynthia Christensen says

      December 23, 2024 at 6:39 am

      If you used volume measures instead of weight it may have remained sticky, but I’m glad that it worked out in the end!

      Reply
Picture of the author with a banner, stating welcome to my blog I am Cynthia.

In our house we get up with the sun, and most of us don't stop working until late in the night, so breakfast and brunch are our family meals. So join me at the kitchen counter, where I cook up delicious food for my busy family, starting first thing in the morning!

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