Activate the yeast. In a bowl, combine warm water, honey, and yeast. Stir and let sit 5 minutes until foamy. If it doesn't foam, your yeast ghosted you—start over.
Make the dough. Add whole-wheat flour, bread flour, salt, and olive oil. Mix until a shaggy dough forms. Rest 10 minutes to hydrate the wheat (autolyse = softer texture).
Knead to smooth. Knead by hand 5–7 minutes (or stand mixer 4–5 minutes) until slightly tacky and elastic. Lightly oil a bowl, place dough inside, cover, and rise 45–60 minutes in a warm spot until doubled.
Prep the garlic oil. Stir together olive oil, garlic, Italian seasoning, red pepper flakes, and salt. Set aside to let the flavors bloom.
Prep fillings. Pat veggies dry. Toss mozzarella with Parmesan and oregano. Keep sauce thick—waterlogged sauce equals soggy regrets.
Pizza Muffins. Grease a standard 12-cup muffin tin. Punch down dough and divide into 12 equal pieces. Press each into a rough 4-inch round. Place into muffin cups, making a small well in the center.
Fill the muffins. Add 1–2 teaspoons sauce, a generous pinch of cheese mix, and chosen toppings. Pinch edges toward the center to partially cover. Brush tops with garlic oil.
Pizza Roll Bites. Roll dough into a 12×8-inch rectangle. Spread a thin swipe of sauce (leave edges clean), sprinkle cheese and toppings. Roll tightly from the long side. Freeze 10 minutes for cleaner cuts, then slice into 12–16 rounds. Place on parchment-lined sheet, spiral facing up. Brush with garlic oil.
Proof briefly. Let shaped muffins or roll bites rest 15–20 minutes while the oven preheats to 425°F (220°C). This relaxes the dough for a lighter bite.
Bake. Bake 13–17 minutes until puffed, golden, and cheese is bubbling. Muffin tins may run a minute longer than sheet pans; trust your eyes and nose.
Finish like a boss. Brush with remaining garlic oil, dust with Parmesan, sprinkle basil, and a tiny pinch of flaky salt. Cool 5 minutes so the molten cheese doesn't brand your soul.
Serve. Offer extra warm pizza sauce or marinara for dipping. Warning: they vanish fast—stash two for yourself first.