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Healthy & Easy Pizza Muffins

These pizza muffins are everything you love about pizza, but in a bite-sized snack you can take on the go!

Sure, you could make pizza bagel bites if you truly want bite-sized pizza, but these are even better.

Every pizza muffin is stuffed with sauce & gooey cheese, leveling them up from boring “regular” muffins.

If you know anything about me, you know how much I love pizza. I spent months trying to master my Neapolitan Pizza Recipe, and it has since become a weekly staple in my house (we’ll never miss an opportunity to celebrate Pizza Friday).

But there is just something about having a quick, easy recipe in your arsenal. Being able to whip these pizza muffins up in just 30 minutes is going to be something I turn to on a regular basis going forward.

Even if you’re not a baker, I promise you these pizza muffins are very easy to put together! And if you have kids, this is a great recipe to make with them!

How do you make pizza muffins?

The process for making these muffins is quite simple!

First, we’re going to throw flour, baking powder, and some seasoning into a large bowl.

Then, we’re going to mix in some plain nonfat Greek yogurt until it becomes a light crumble. If that sounds weird or gross to you, don’t worry! I happen to hate the taste of plain Greek yogurt, but it’s a magical ingredient when mixed with flour. If you need proof, check out my 2 Ingredient Protein Bagels.

The last step to making the dough is throwing in our light butter- I do this by spreading small pieces throughout the bowl for easy mixing. “Light butter” is simply a buttery spread that has half the calories of full-fat butter. I used “Country Crock” if you want to use the same one!

Once you mix everything up with the butter, you’ll have a beautiful ball of dough for the pizza muffins!

Separate that dough into 6 pieces to start prepping the pizza muffins.

I like to use silicone baking mats to form the muffins, but you can do it on the counter as well. Just be sure to add a little bit of extra flour to make it easier on you since the dough will be a bit sticky.

We’re going to make small cavities in each pizza muffin for the filling. These muffins aren’t gigantic, so don’t worry about trying to make the cavities as large as possible.

Then, we’re simply filling the pizza muffins with a little bit of pizza sauce and mozzarella cheese.

Be careful not to over-fill the pizza muffins!

I only used a very small amount of pizza sauce and cheese- a little bit goes a long way. We need to be able to close these up, so you don’t want to get too aggressive with the filling.

Once the filling is in, we need to take the sides and pinch them up at the top. As you can see by my example, some sauce is going to squeeze out, and that is totally fine! They do not need to be perfect by any means.

Pick up each ball in your hands and pinch closed any openings to make sure all the cheese stays inside the pizza muffins.

Then, we’re going to put each ball with the pinched side down in our cupcake/muffin liners. If you do not have any liners, you can just use the pan, but make sure to spray it! Putting the pinched side down is very important here so they do not open up while baking.

All that’s left to do is top with some additional sauce and shredded mozzarella cheese! I was pretty conservative with mine because I was worried about making a mess- feel free to be a little bit more generous with the sauce & cheese on top of your pizza muffins.


What can you use as toppings for pizza muffins?

I kept my own pizza muffins simple- just sauce and cheese. However, you can top them (and fill them) however you want! Here are some ideas:

  • Stuff with ricotta cheese
  • Stuff with cheese & sauce and top with butter & garlic
  • Add pepperoni to the stuffing and topping
  • Fill with a chunk of mozzarella instead of shreds for the ultimate gooey-ness

You could probably turn these into breakfast muffins as well, but I have a specific recipe for that. They’re not quite muffins, but my Breakfast Bagel Bombs are one of my most popular recipes on the blog, and will satisfy your breakfast craving!


Can you make substitutions for pizza muffins?

Substitutions can be tricky as there are specific reasons why I use each ingredient, so let me break down the main ingredients and what you could possibly use as a substitution.

All-Purpose Flour

You should be able to substitute whole wheat flour, and most likely a 1:1 gluten-free flour as well. However, you will not be able to use almond flour or coconut flour. The all-purpose flour gives these pizza muffins their structure, so it’s necessary.

Light Butter

This is an ingredient you have lots of room to play with! I use “Country Crock” which is just a buttery spread with 50 calories per tablespoon. Any fat source should work here: full-fat butter, coconut oil, vegan buttery spread… it should all be safe. Obviously, the taste (and calories) will change slightly depending on what you use, so I recommend something with a buttery flavor if you can help it.

Sugar Substitute

The tiny bit of sweetness really helps not only the flavor, but also the structure of these pizza muffins. You can use any granular sweetener you want- even regular sugar. I haven’t tried without any sweetener (I learned how well it works when I made my Pretzel Biscuits) but it may still work fine. Just don’t try to use a liquid sweetener as it will mess with the consistency of the dough too much.


You can use any seasoning you want for these pizza muffins! The only one that is necessary is salt- otherwise, you can change up the seasoning and quantities. I wouldn’t recommend leaving the garlic powder out, since everything is better with garlic (especially pizza), but I won’t judge.


Can you store leftover pizza muffins?

You sure can!

These pizza muffins didn’t last very long in my house, but we did have a few left over.

I stored these in Tupperware in the fridge, then simply microwaved each pizza muffin for about 15 seconds prior to eating, and they were good as new!

I would say that these should stay fresh in the fridge for about a week, but I seriously doubt they’re going to make it that long.



Pizza Muffins

Pizza Muffins

Yield: 6 Muffins
Prep Time: 10 minutes
Cook Time: 25 minutes
Total Time: 35 minutes

These muffins are all the deliciousness of a pizza, but in a light muffin that you can take on the go with you anywhere! No yeast, no advanced prep- just make, bake, and enjoy!


Muffin Ingredients

  • 150g All-Purpose Flour
  • 1 1/2 Tsp Baking Powder
  • 120g Plain Nonfat Greek Yogurt
  • 42g Light Butter / Buttery Spread
  • 15g Granular Sugar Substitute
  • 1/4 Tsp Salt
  • Pinch of Pepper
  • 1/2 Tsp Garlic Powder
  • 1/4 Tsp Italian Seasoning

Topping & Filling

  • 42g Shredded Mozzarella Cheese
  • 30g Pizza Sauce


  1. Preheat the oven to 350 degrees F
  2. Add the flour, baking powder, and seasonings to a large bowl, then mix those up.
  3. Add the Greek yogurt and mix together until it begins to form a light crumble.
  4. Spoon pieces of the buttery spread (or cut your butter) into the bowl so they are spread throughout and not just in one large piece. Use a silicone spatula to mix everything together until a dough forms.
  5. Remove onto a lightly floured surface and divide the dough into 6 equal-sized pieces. If you want them to be uniform, you can weigh your entire ball of dough and divide that by 6 to get the exact weights for each.
  6. Roll each piece into a ball and form a cavity in the center for your fillings.
  7. Spoon some of the pizza sauce into the cavities. You do not need to use a lot here- just enough to coat the inside. Then, add some mozzarella cheese to each.
  8. Lightly flour your hands to help with the sticking, and then pinch the sides of the dough balls up to cover the filling. Pick up the dough ball to form it into a ball, making sure to pinch closed any openings.
  9. Place each dough ball with the pinched side down into a cupcake/muffin pan with liners (if you do not have liners, make sure to spray with nonstick spray).
  10. Spoon some additional sauce on top of each muffin, then top with some more shredded mozzarella cheese.
  11. Bake for 25 minutes, then remove and enjoy!


  • If you do not want to stuff the muffins, you can skip that step and just top with sauce & cheese instead. However, the stuffing helps add moisture (not to mention a ton of flavor)
  • Be careful not to stuff the muffins too much with sauce- a little goes a long way from what I learned.
  • The sugar in the dough sounds odd, but I promise you will not taste it.
  • I stored these in a sealed container in the fridge and enjoyed the leftovers throughout the week. Microwaving for about 15 seconds did the trick!
Nutrition Information
Yield 6 Muffins Serving Size 1 Muffin
Amount Per Serving Calories 150Total Fat 5gCarbohydrates 20gProtein 6g

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Wednesday 13th of January 2021

Question, if I truly needed to, could I use regular sugar? Would that impact the recipe?


Wednesday 13th of January 2021

Most definitely you can! It should have zero impact vs the sugar substitute except for adding a teeny amount of extra calories

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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