The boys have been going gaga for these gluten-free Pizza Muffins. They eat them for breakfast, in their lunches, and as a healthy after school snack. Since I’ve been cutting back on my sugar intake I’m a big fan of these pizza muffins too. For me, they’re sort of like a savory cupcake. Cute and little, with adorable decorations on top –everything I want a cupcake to be, without the sugar.
In order to make the adorable miniature pepperoni slices that top these Pizza Muffins, I stacked up pieces of pepperoni and pressed down on them with the small side of a metal funnel. Works like magic!
Although my boys are now teenagers, I think they would have loved cutting out the tiny pieces of pepperoni and decorating the tops of these muffins with me when they were small children. Those were the fun types of projects we used to do together. Now when we’re in the kitchen, rather than collaborating on one dish together, we make separate dishes and collaborate on making one big meal. My favorite time with the boys is still kitchen time. I love watching them cook (and clean), and seeing them take pride in everything they make!
Pizza Muffins

Ingredients
- 1½ cups blanched almond flour (not almond meal)
- ½ teaspoon celtic sea salt
- ½ teaspoon baking soda
- 4 large eggs
- ¼ cup tomato sauce, plus ¼ cup for topping
- ½ cup cheddar cheese, plus ½ cup for topping
- ½ cup parmesan cheese, plus ½ cup for topping
- 2 ounces pepperoni, plus 2 ounces for topping
Instructions
- In a food processor, combine almond flour, salt, and baking soda
- Pulse in eggs and sauce until combined
- Pulse in cheeses and pepperoni
- Line 12 muffin cups with paper liners
- Scoop a heaping ¼ cup of batter into each cup
- Bake at 350°F for 25 minutes
- Remove from oven; place 1 teaspoon sauce on top of each muffin
- Sprinkle cheese over sauce
- Sprinkle pepperoni over cheese
- Place back in oven and bake for 15 more minutes
- Cool for 1 hour
- Serve
I based this recipe on one from Pamela Salzman, a private chef in Southern California. I haven’t tried it, but I’ll bet this grain-free Pizza Muffin recipe would be incredible with various vegetable fillings and toppings such as mushrooms, spinach, or zucchini. If you experiment, please let us know what changes you make to the recipe and if you have to adapt any of the other ingredients. When you include vegetables it may be best to saute them first, otherwise they will be very wet.
I tried making these Pizza Muffins with more tomato sauce on top and preferred them with the one teaspoon indicated in the recipe. I found they became a tad soggy when I increased the tomato sauce to two teaspoons.
I haven’t tried making these Pizza Muffins dairy-free as my boys can eat cheese. If you do play with the recipe and remove the cheese please tell us how it goes! How will you customize this recipe to make your very own pizza muffin?








Gail H says
How to prepare for a possible hurricane: make these muffins! Elana, one of your best recipes yet. I just had my first taste (couldn’t resist). I used Asiago and Parmesan freshly grated for the topping with the funnel cut pepperoni. I am ready for any storm or flooding here in coastal NJ. Thanks!
Carolyn says
Thanks for the recipe which will slow down insulin spikes, and thanks for this formatting. I print out in black & white because it is less expensive.
Liza says
Hi Elana,
These look great! They would be perfect for my son to take to school. Unfortunately, my son’s school (as well as many other schools and preschools nowdays) has a nut free policy. Have you by any chance tried to make these with coconut flour?
Thank you
Elana says
Liza, I haven’t, if you do please let us know how it goes!
Debbie Weddle says
Im allergic to eggs, what would be a good substitute for that?
Silo Dog says
Ener-G egg replacer
Hannah M. says
I have tried Chia seeds as a substitute and it works really well. You grind up 1 tablespoon of Chia seeds, mix in 3 tablespoons of water and you’ll get a mixture with the consistency of a raw egg.
Cindy says
I am allergic to almonds as well and need GF as well and would like to know of a substitute. I do a lot with coconut but I realize you would need something else with it but I am not knowledgeable enough to know what to do with this.
Elana says
Hi Cindy, I wish it was that simple! By removing any of the main ingredients and replacing them with another you are creating a new recipe that will need testing. If you do undertake this project I hope you’ll stop back by to let us all know how it goes :-)
Liesbet says
Try the recipes from Ine Reynierse – Low Carb Is Lekker (South African). She also uses almond flour, but it can be substituted with pecan nut flour, ground pumpkin seeds, … . She has a blog, but also a hard copy cook book which has been in the top selling list for non-fiction for weeks here in SA.
Angela says
I have an allergy to almonds as well. I use gf oat flour in place of almond flour.
Sarah says
What is your opinion on buckwheat as a substitute for almond flour?
Elana says
Sarah, I haven’t ever cooked with buckwheat flour. I’ve been grain-free since 2001 and during this time have avoided all grains and grain-like foods. If you try it though please let us know if it works!
Christine says
Buckwheat flour will be very heavy, and give this a nutty flavor that may not sit well. Although I know buckwheat is a seed, it still sits very heavy in my tummy.
I would recommend cassava root flour, or tapioca, but not the same as tapioca starch. You can try Chebe “bread” mixes (just look up “Chebe” on Amazon). Also, teff flour is pretty good too.
Leianne Taylor says
Elana,these muffins look and sound delicious! Friday night is pizza night at our house. I’m looking forward to trying them.
Elana says
Leianne, I hope your family enjoys them as much as mine does!
Cheryl Palos says
I’ll use my muffin top pan for these! Yum!
Elana says
That is an amazing idea Cheryl! Please stop back by and let us know how they turn out :-)
Gabriele says
What is a muffin top pan?
K2 says
It makes a baked good like the top of the muffin that people pull off to eat first. It’s also the perfect size for a small burger bun and that makes me wonder if this would make a good sandwich bun. Hmmm. I’ll definitely have to try that.
Elana says
Thanks K2!
Catriona Gladman says
Elana, thankyou for your timing in publishing this. Term 3 starts for us next week here in Australia. I am new to the Paleo diet and am searching for recipes that I can include for my children’s lunchboxes. These Pizza Muffins sound ‘delish’ and will be introduced with great hopes. Wish me luck…
Elana says
Catriona, you’re very welcome!
BarbaraDH says
I’m allergic to almonds. Is there another kind of GF flour I could use as a substitute in this recipe?
Elana says
Barbara, I haven’t tried that, if you do please stop back by and leave a comment to let us know if it worked!
Mette says
Other people have successfully substituted almond flour for sunflower seed flour (1:1) in their paleo bread recipes. I have not tried it with this recipe, but could be an option. Put in a bit of lemon juice to avoid getting green muffins due to the reaction between sun flower seeds and baking soda
Noreen Rhoades says
I bought some millet flour. You would have to determine how much to use for this recipe. It is Bob’s Red Mill.