Combine warm water, yeast, and honey. Let stand for about 5 minutes until foamy.
Add whole-wheat flour, olive oil, and salt. Mix until a dough forms.
Knead for 5–7 minutes until reasonably smooth and elastic.
Place the dough in an oiled bowl, cover, and let rise for 60–90 minutes.
Meanwhile, cook the ground beef in a skillet until fully browned. Drain excess fat.
Add the chicken sausage and cook until lightly browned and heated through.
Cook the mushrooms and bell pepper in olive oil until slightly softened. Add garlic during the final minute.
Preheat the oven to 425°F (220°C).
Oil a 9- or 10-inch deep-dish pan or cast-iron skillet.
Press the risen dough across the bottom and up the sides of the pan.
Spread the tomato sauce over the dough.
Add the ground beef, chicken sausage, and turkey pepperoni.
Add the mushrooms, bell pepper, and garlic.
Top evenly with mozzarella.
Sprinkle with oregano, basil, rosemary, red pepper flakes, and black pepper.
Bake for 20–25 minutes, until the crust is golden and the cheese is melted and bubbling.
Remove from the oven and let rest for 8–10 minutes.
Slice and serve warm.