Cream Cheese Stuffed Everything Bagel Bites

Last Updated on June 15, 2023 by Kayla Berman

Everything Bagel Bites are my new favorite quick and easy breakfast recipe! Made with only a 4 ingredient dough (greek yogurt, flour, baking powder, and salt) these cream cheese stuffed bagel balls are soft, chewy, flavorful, and delicious. They require no yeast and no boiling to make, which means you’ll have a batch of these golden mini bagels ready to go in well under 1 hour!

Need more everything bagel seasoning in your life? Stop by my Everything Bagel Cream Cheese Stuffed Mini Peppers next.

cream cheese stuffed everything bagel bite with a bite taken out

Why You’ll Love Cream Cheese Stuffed Bagel Bites

When someone asks me what my favorite food is, I usually say pasta. Which is true!

But the real, even truer, answer is that I have a favorite food genre. Category if you will. The category is any carb and cheese combination. I literally live for these!

Mac & cheese, quesadillas, grilled cheese, chips and queso, and …. yes, you guessed it! Bagels with cream cheese. One of my favorites of the favorites! However, we all know that the pairing of carbs and cheese – although delicious – is not the best for us.

So when I came across the viral 2 ingredient (greek yogurt and flour) bagel dough that is a better-for-you alternative to the classic boiled and baked doughnut-shaped roll, I was floored! I simply had to try it out.

I did. And then I thought … you know what would make this even better? If they were bite-sized, smothered in everything seasoning, and stuffed with cream cheese. Thus, Cream Cheese Stuffed Everything Bagel Bites were born!

They are my carb and cheese dream come true. Here’s why I love them:

  • Easy To Make: Cream cheese bagel bites do not require any boiling, yeast, or waiting for dough to rise! This makes them much easier to make than classic bagels. You can have a hot and fresh batch ready in under 1 hour.
  • No Bagel Shop Needed: There is nothing I love more than a weekend morning bagel! I head to the bagel shop on a Saturday or Sunday and enjoy one of my favorite meals of the week. Now, with these stuffed mini bagels, you don’t need to leave your kitchen to get the same effect! You also don’t need to drive through Dunkin’ Donuts or Starbucks to get their poppable bites.
  • Delicious: Duh! Soft, tender, and chewy everything-seasoned mini bagel balls stuffed with an ooey-gooey, melty cream cheese center is pretty much my definition of delicious.
  • Good-For-You: Now I am not a dietician or nutritionist, but in my opinion these greek yogurt bagel bites are a nutritious, better-for-you alternative than the classic morning carb. They are under 100 calories each, with 5 grams of protein. That is a win in my book! Note: I do use reduced fat cream cheese, so regular cream cheese would make that info a little different.
  • Customizable: Read the full post below for how you can create endless bagel varieties from this base recipe. You can switch up the cream cheese, filling, and seasoning mix to your heart’s delight!
cream cheese greek yogurt bagel bites on a white plate with everything seasoning on the side

Ingredients & Substitutions

These homemade bagels are made with just a 4 ingredient dough! How crazy is that? You probably already have most of the ingredients required in your pantry too.

Just add in the two most important bagel pairings – plain cream cheese and everything seasoning – and you are good to go. Here is the breakdown of exactly what you’ll need:

  • Flour: The base of this wonderfully chewy bagel bite recipe is all purpose flour. You will need 1 cup!
  • Greek Yogurt: You’ll need equal parts yogurt and flour for this recipe. Therefore, add 1 cup plain greek yogurt. Fage non-fat will work best!
  • Baking Powder: Since this recipe doesn’t require any yeast, you have to replace it with a different leavening agent. Baking powder does the trick! Add 2 tsp to give these little bagel bites the perfect rise.
  • Salt: Add 1/2 tsp salt to the bagel dough for an extra oomph of flavor.
  • Cream Cheese: Stuffing these bite-sized bagels with a little bit of ooey-gooey, melty cream cheese takes this popular breakfast to a whole new level. It is incredible! You’ll need about 5 tbsp of your favorite cream cheese.
  • Everything Seasoning: Last, but most certainly not least you’ll need some everything bagel seasoning blend. There is no exact measurement, just however much you’d like!

Grab that short 6 ingredient grocery list and let’s get cooking!

Equipment Needed

This post contains affiliate links. As an Amazon Associate, I earn from qualifying purchases. 

everything bagel bite ingredients measured out on a white table

How To Make Everything Bagel Bites

Cream cheese bagel bites are extremely easy to make! You can have the perfect soft, chewy, and delicious stuffed bagel minis ready in no time, right in your own kitchen.

No bagel shop, yeast, boiling, or letting dough rise needed!

Step 1: Heat oven. Set the oven to 375 degrees.

Step 2: Combine dry ingredients. Add the all purpose flour, baking powder, and salt to a large mixing bowl. Whisk to combine thoroughly.

Step 3: Form dough. Add in the greek yogurt.  Use a spatula to combine the ingredients until a dough forms.

Step 4: Knead dough. Remove the dough ball from the large bowl and transfer to a lightly floured surface.  Knead the dough by hand for about 1-2 minutes.  

Step 5: Divide dough. Next separate the dough into 8 equal portions.  I first divide the dough into quarters, and then split those quarters in half.

Step 6: Add cream cheese. Line a baking sheet with parchment paper and add nonstick cooking spray.  Take each dough ball and flatten it into a circle, then place on the parchment paper.  Once all dough balls are added, divide the cream cheese among them.  Add about 2 tsp of cream cheese to the center of each dough circle.

Step 7: Form dough balls. Next wrap the dough around the cream cheese filling for each bagel bite. I recommend taking the edges of the dough and folding into the center and then pinching them closed. Place the pinched side down on the baking sheet.

Step 8: Add egg wash & seasoning. Once all the bagel bite dough balls are formed, top each one with the egg wash.  Sprinkle as much everything bagel seasoning as you’d like on top of each one.

Step 9: Bake. Bake for 25 – 27 minutes, until golden brown.

Step 10: Serve & enjoy! Remove from the oven and allow the bagel balls to cool slightly. Serve and enjoy!

white plate with stuffed bagel bites

Optional Variations & Dietary Adaptions

Stuffed everything bagel bites are truly perfect just the way they are. Like out-of-this-world delicious! But you could always make adjustments to the recipe to meet your personal tastes, preferences, or needs!

Here are some of my ideas for dietary or flavor adaptions:

  • Cream Cheese: I used plain cream cheese in these bagel bites, but you could use any kind of cream cheese you’d like. You could make your own flavored cream cheese by mixing in some green onion or chives. But you could also just use any store bought flavor. Perhaps veggie, garlic and herb, or strawberry cream!
  • Make ‘Em Sweet: I think a sweet variation of these stuffed bagels would be fantastic! Perhaps mix a little maple syrup into your cream cheese filling and add a coating of cinnamon sugar instead of everything seasoning. YUM!
  • Different Flavors: These are everything bagel balls of course, but you could make a version of this recipe for any flavor bagel you like. Poppy, sesame, or plain bagels would be super simple – just replace or leave off the everything seasoning. But you could go even crazier! Make cheesy jalapeño bites by adding a sprinkle of cheddar cheese or mozzarella cheese and jalapeño slices on top. Try cinnamon raisin or chocolate chip too – just mix the extra ingredients right into the dough. You could even just add extra flavors and seasonings on top with garlic powder, Italian seasoning, or flakey salt!
  • Make Them Bagels: Want to make regular sized bagels instead of bagel minis? No worries! This chewy bagel dough works perfectly for either. Follow the same instructions up to step 4, then at step 5 only divide the dough ball into 4 equal pieces. Take each piece and roll out into a long log shaped piece of dough. Take the ends of the log and fuse together to form a bagel shape, a circle with a hole in the middle. Then continue with the egg wash, adding seasoning, and baking!
  • Gluten Free: These cream cheese bagel bites can easily be made gluten free. All you have to do is swap in a gluten free flour! I would recommend using a 1:1 replacement flour, like Bob’s Red Mill.
  • Vegan: You can also make this recipe dairy free or vegan if need be. For both dairy free and vegan, use a thick dairy free yogurt and a dairy free cream cheese substitute. For vegan bagel bites, you’ll also need to skip the egg wash or replace it with aquafaba (liquid from a can of chickpeas) or melted vegan butter.
  • Add More Stuffing: Now I have not tested this, but I think it would be fun and delicious to stuff more ingredients into these little bagels. Perhaps berries, fruit jam, or chocolate chips for sweet. And bacon for savory! I’m drooling just thinking about it.
greek yogurt bagel bite cut in half with the inside cream cheese filling showing

Expert Tips

If you follow the tips below you are sure to bake the perfect bagel bites – golden, flavorful nuggets filled with delicious cream cheese – each and every time!

  • In order to get soft, fluffy, and tender bagel bites make sure your baking powder is not expired. I find that this is an ingredient that sometimes sits in people’s pantries (mine included) for years and could expire without them knowing! Just make sure yours is fresh and working well to give these mini bagels the best results.
  • I have tried spreading both just an egg white wash and a full egg wash on top of these bagels, and the egg white just doesn’t have the effect I am going for. The yellow yolk in a whole egg wash is what helps achieve that beautiful golden brown top. I highly recommend you do not skip it! And use a pastry brush to apply.
  • When kneading the dough and rolling into balls, flour your hands and the clean work surface that you will be using. This will help prevent sticking!
  • Do not add too much cream cheese to the center of each bagel bite. If you add too much you will have difficulty closing the dough around it. Stick to the instructed 2 tsp ish!

Serving Suggestions

I would personally enjoy bagels at each and every time of day. Not only would I … but I do!

Especially these easy greek yogurt bagel bites. They get bonus points for being more nutritious and protein packed then your classic bagels! Which means I feel great about eating them for breakfast, lunch, and as snacks throughout the day.

I certainly do not need a reason to prepare myself a batch of these golden, cream cheese stuffed bagel balls – but I understand if you need some convincing on how you could serve and enjoy them!

Here are some fabulous serving suggestions:

  • Add To A Brunch Spread: This recipe would make a great addition to any breakfast party or brunch celebration spread. I am pretty sure everyone in the whole world loves a warm bagel and cream cheese to start their day – and if you don’t you are definitely not invited to my brunch LOL – so these are bound to be a hit with everyone you serve them too. Pair with my Spinach & Veggie Egg White Frittata for some veggies, Crescent Roll Monkey Bread for a sweet treat, and Chicken Maple Breakfast Sausages for extra protein!
  • Meal Prep: Nothing can get me out of bed quite like knowing that I have cream cheese stuffed bagel bites waiting for me downstairs. All that is between me and the best first bite of food for the day is 5 minutes in the toaster oven or 60 seconds in the microwave! Plus these bagel bites have around 90 calories and 5 grams or protein each (I use reduced fat cream cheese), which is pretty good for a carby cheesy breakfast if you ask me. If you’re looking for more recipes to meal prep to make your week a bit easier, check out my Ground Turkey Teriyaki Bowls for dinner and my Chocolate Strawberry Yogurt Clusters for a healthy dessert.
  • Make For Your Kids: I do not personally have kids, but I can almost guarantee that these would be a hit with them! I know my baby cousins love the bagel bites from Dunkin’ Donuts and Starbucks, so since these bites are a copycat of those … I’m sure they would eat them right up. And if you’ve got picky eaters, just leave off the everything seasoning! These stuffed mini bagels would make the perfect quick breakfast, easy addition to a lunchbox, or scrumptious after school snack. Plus you could even prepare them with your kids as a fun hands on activity.
everything mini bagel bites

FAQs

Where can I buy everything bagel seasoning?

You can buy everything bagel seasoning in most grocery stores! It will be in the aisle with all other spices and seasoning mixes.

If you can’t find in your local store, you can also purchase online. Here is one from Amazon!

You can even purchase Trader Joe’s Everything but the Bagel Seasoning Blend online which I’ve heard is one of the best options out there.

Can I make my own homemade everything seasoning?

Yes, you absolutely can. Everything seasoning is simply a combination of poppy seeds, sesame seeds, dried garlic, dried onion, and salt.

You may even have all of these elements in your pantry already. Just combine them to make the flavorful and delicious blend, most famous for its use on bagels!

But once you make the blend, you could use it on so much more than just the breakfast food – roasted vegetables, garlic knots, and roasted salmon or chicken thighs.

Check out this post for more detailed measurements and instructions on how to make the seasoning blend in your own kitchen!

Which type of greek yogurt should I use in these bagel bites?

I recommend using Fage 0% Milkfat Plain Greek Yogurt! It is what I use and have gotten great results every single time.

How to best store this recipe?

Although these little bagel balls are best enjoyed hot and fresh out of the oven, as any bagels are, you can store leftovers in an airtight container in the refrigerator. They will keep for 3-5 days!

Then to reheat pop in the oven, air fryer, or microwave for 5-10 minutes until warmed throughout.

Can I freeze these stuffed bagel bites?

Yes, you can! Transfer the bites to a freezer safe container or bag and place in the freezer. They will keep for a couple of months.

Then you can follow the re-heating instructions above when you’d like to enjoy!

cream cheese stuffed bagel bites on a plate with one opened in half

Related Recipes

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Connect With Me!

If you make this everything bagel balls recipe or any of my other recipes, I would absolutely love to know! Tag me @wellnessbykay on Instagram so I can see and share your recreations.

cream cheese stuffed bagel bite with a bite taken out of it

Love this recipe? Leave a comment and a rating! I love to see and it helps me continue to develop delicious recipes for this blog.

Print

Cream Cheese Stuffed Everything Bagel Bites

Everything Bagel Bites are my new favorite quick and easy breakfast recipe! Made with only a 4 ingredient dough (greek yogurt, flour, baking powder, and salt) these cream cheese stuffed bagel balls are soft, chewy, flavorful, and delicious. They require no yeast and no boiling to make, which means you’ll have a batch of these golden mini bagels ready to go in well under 1 hour!

  • Author: Kayla Berman
  • Prep Time: 15 Minutes
  • Cook Time: 25 Minutes
  • Total Time: 40 minutes
  • Yield: 8 Bagel Bites 1x
  • Category: Breakfast
  • Method: Baked

Ingredients

Scale
  • 1 cup plain greek yogurt
  • 1 cup all purpose flour
  • 2 tsp baking powder
  • 1/2 tsp salt
  • 5 tbsp cream cheese, about 2 tsp in each bagel bite
  • 1 egg, beaten for egg wash
  • Everything bagel seasoning

Instructions

  1. Set the oven to 375 degrees.
  2. Add the all purpose flour, baking powder, and salt to a large mixing bowl. Whisk to combine thoroughly.
  3. Add in the greek yogurt.  Use a spatula to combine the ingredients until a dough forms.
  4. Remove the dough ball from the large bowl and transfer to a lightly floured surface.  Knead the dough by hand for about 1-2 minutes.  
  5. Next separate the dough into 8 equal portions.  I first divide the dough into quarters, and then split those quarters in half.
  6. Line a baking sheet with parchment paper and add nonstick cooking spray.  Take each dough ball and flatten it into a circle, then place on the parchment paper.  Once all dough balls are added, divide the cream cheese among them.  Add about 2 tsp of cream cheese to the center of each dough circle. See the full post for photos.
  7. Next wrap the dough around the cream cheese filling for each bagel bite. I recommend taking the edges of the dough and folding into the center and then pinching them closed. Place the pinched side down on the baking sheet.
  8. Once all the bagel bite dough balls are formed, top them with the egg wash.  Sprinkle as much everything bagel seasoning as you’d like on each one.
  9. Bake for 25 – 27 minutes, until golden brown.
  10. Remove the bagel balls for them oven and let cool slightly. Serve and enjoy!

Keywords: everything bagel bites, cream cheese bagel bites, stuffed bagel bites, cream cheese stuffed bagel bites, greek yogurt bagel bites

This post may contain affiliate links, which if a product is purchased through I may recieve a small compensation. I only recommend products I love and use in my life and cooking! Thank you for supporting wellnessbykay.

9 Comments

  1. In trying to print this recipe, I was unable to view ALL of the recipe when printed because the ads on the recipe page obscure the recipe!!
    I’m extremely disappointed.

  2. I tried to do a Keto version by using almond flour. It didn’t work; even with an extra half cup of flour it didn’t make dough. HOWEVER … even though they turned out to be flat pucks instead of balls, and very crumbly, they were delicious! Like biscuits. We buttered the top and sprinkled with more everything seasoning and I am truly addicted. I’m sorry I couldn’t rate your recipe as is; I was really hoping it would work. But I wanted you to know this is the BEST keto bread I have found to date!

  3. Is the dough supposed to be that sticky? I had a hard time working with it. They are baking now, so I’m reserving rating until we taste them.

    • Kayla Berman

      Hi Beate! Yes, the dough will be quite sticky. Hopefully the recipe turns out well for you! 🙂

    • So sticky that I gave up. I lost almost half of it because of the amount stuck to the floured surface, hands and scraper. I even added another 1/4 c if flour and it was still uncontrollable.
      Epic fail.

  4. Finally got to make these, delicious!!

  5. Second batch in the oven now. Strawberry cream cheese sprinkled on top with powdered sugar!! Great recipe!!

  6. Love this recipe, made three times already. Just one question, does it has to always be Greek yogurt? Can it be plain yogurt or any other substitute? I love them the way they are just checking for more options.

  7. Joanne Girard

    Can I freeze them before baking them?

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