Hot Honey Pizza Muffins (Made With Einkorn Flour)
These hot honey pizza muffins are cheesy, savory, and melty: Like personal-sized deep dish pizzas baked in muffin tins. Each one is loaded with cheese and pepperoni and drizzled with sweet-spicy hot honey. The crust is made with wholesome einkorn flour, an ancient grain that adds rich, nutty flavor and extra nutrition.

I’ve been baking a lot with Grand Tetons Ancient Grains lately, and I’m thrilled to partner with them for this post. The all-purpose einkorn flour gives these pizza muffins a depth of flavor and texture you just can’t get with regular flour.
My favorite new food at the Minnesota State Fair this year was the hot honey pizza balls from Green Mill. The pizza balls were filled with cheese curds, pepperoni, Parmesan cheese, and herbs, surrounded by a buttery crust, and finished with a drizzle of hot honey.
Even after a day of heavy eating, this new fair food was something we couldn’t stop eating. We finished the whole order.
So naturally, I had to try to recreate this dish at home.

About The Recipe: Hot Honey Pizza Muffins
These hot honey pizza muffins with einkorn pizza crust are the perfect bites for an appetizer or dinner.
You’ll start out by making a simple pizza crust with einkorn flour. Since we’re using instant yeast, there’s no rising time required. You’ll cut the dough into 12 equal pieces, shape into rounds, and press into a buttered muffin tin.
Then you’ll load the cups with toppings: Pizza sauce, pepperoni, and mozzarella cheese.
The cups are baked until golden brown and bubbling hot.
The chef’s kiss is a drizzle of hot honey.
Sweet, savory, cheesy, hot – all in one bite.
Scroll down for detailed recipe.

What You’ll Need
The ingredient list for these einkorn pizza muffins is short and simple:
For the crust:
- All-purpose einkorn flour (I purchase mine from Grand Teton Ancient Grains)
- Instant yeast (Note: I have rapid-rise yeast pictured in the ingredient photo, but please use instant yeast!)
- Sugar
- Olive oil
- Water
For the toppings:
- Pizza sauce
- Mozzarella cheese (grate your own from a block of mozzarella cheese for best results)
- Pepperoni
- Hot honey (purchase or make your own)
Assembling The Pizza Muffins
Once you make the dough, the process of making the muffins pizzas is pretty quick and easy:
- Divide dough into 12 equal pieces
- With floured hands, flatten dough into a round
- Place dough into buttered muffin tin slot, removing any excess that extends beyond the top of the slot
- Fill each slot with pizza sauce, 2 pepperoni slices, mozzarella, 2 more slices of pepperoni, and more mozzarella

Why Bake With Einkorn Flour?
If you haven’t baked with einkorn flour before, you’re in for a treat. Einkorn is the world’s most ancient form of wheat: a pure, unhybridized grain that’s remained virtually unchanged for thousands of years. It has a naturally light, nutty flavor and gives baked goods a soft, tender texture with a warm golden hue.
For this recipe, I used Grand Teton Ancient Grains All-Purpose Einkorn Flour, freshly milled in small batches in Idaho. Their flour is simple and pure – nothing added, nothing removed – and it’s always unbleached, unbromated, and free from glyphosate or other chemicals.
Unlike most store-bought all-purpose flours, this one still includes the germ, which gives it extra flavor, nutrients, and that signature golden color. It’s milled on a dedicated einkorn mill, meaning no cross-contamination with other grains, and you can even find the mill date printed on the bag for freshness.
If you’re curious about trying ancient grains, einkorn is one of the easiest and most rewarding to bake with. It behaves a little differently than modern flour (more delicate dough, slightly stickier), but once you get used to it, you’ll love the results, especially in recipes like these Hot Honey Pizza Muffins or one of these:

Tips For Success
Want to learn how to make these pizza muffins really, really good? A recipe you’ll put on repeat and add to your dinner rotation? Keep these tips in mind:
- Shred your own mozzarella cheese: Bagged, pre-shredded cheese contains anti-caking agents which can affect the cheese’s melting properties. To make sure the cheese is really good and melty, shred your own from a block of mozzarella cheese. (And start doing this anytime you’re baking with cheese!)
- Don’t overwork the dough: Einkorn flour has a different gluten structure than modern wheat — it’s more delicate. Mix the dough just until it comes together and knead for a short time (a minute or two) for a tender, soft crust.
- Use plenty of butter in the muffin pan: Pizza muffins can stick to the pan easily, so make sure to grease your muffin tin very generously with butter. Bonus: This adds more flavor to the pizza muffins!
Hot Honey Pizza Muffins (With Einkorn Crust)
Make sure to butter the muffin tin well. This makes the pizza muffins easy to remove - and adds great flavor to the crust.
Ingredients
- 3 1/2 cups all-purpose einkorn flour
- 1 teaspoon salt
- 1 teaspoon sugar
- 1 packet instant yeast (7 grams / 1/4 oz.)
- 1 teaspoon olive oil
- 1 cup warm water
- 1 cup pizza sauce
- 48 slices of pepperoni
- 2 1/2 cups shredded mozzarella cheese
- Hot honey, for drizzling
Instructions
- Preheat oven to 425F. Generously butter a 12-slot muffin tin. Set aside.
- Measure einkorn flower and add to a large mixing bowl. Stir in salt, sugar, and yeast. Add olive oil and warm water. Mix until a dough forms.
- On a clean, floured surface, knead dough until it becomes smooth. This should take just a couple of minutes.
- Divide dough into 12 pieces. Using your hands, shape each dough ball into a flat round - about 5 inches in diameter.
- Press dough round into a buttered muffin slot. If the dough sticks to your hands, you can dust them with a little flour. If the dough extends above/beyond the individual muffin slot, remove it. You want each cup to fill - but not extend beyond - the muffin slot.
- Once all of the dough has been placed in the muffin tin, add your toppings: A generous teaspoon of pizza sauce, 2 slices of pepperoni, a tablespoon of cheese, 2 slices of pepperoni, and more cheese on top.
- Bake for 17 to 18 minutes, until crust is golden brown and cheese is bubbling hot.
- Remove pizzas from muffin tin, set on a serving platter and drizzle generously with hot honey.
