Heat the oven to 400 degrees. Place paper liners in a muffin tin or grease with oil spray.
To a medium bowl, add the flour, baking powder, baking soda, salt, and dried herbs, if using. Whisk to combine.
In a large bowl, whisk together the cottage cheese, egg, oil, marinara sauce, and milk.
Add the flour mixture to the bowl and use a large spoon or rubber spatula to mix. Before the the flour is fully mixed in, add the 3/4 cup mozzarella, spinach, and 1/2 of the pepperoni, if using. Continue to mix until everything is just incorporated.
Divide the batter between the muffin cups, filling mostly to the top. Sprinkle a pinch of cheese over each muffin then add a few pieces of pepperoni, if using.
Bake until golden brown on top and cooked through, 12 to 14 minutes.
Once muffins are cool, store in an airtight container at room temp for 1 day or in the refrigerator for 4 to 5 days. The muffins can also be well wrapped and frozen for 1 month.