Preheat oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or spray generously with non-stick spray. This is important—protein powder gets sticky, so paper liners should be sprayed even though regular muffins don't usually need it.
In a large bowl, whisk together all dry ingredients: flour, protein powder, baking powder, baking soda, salt, and cinnamon. Make sure the protein powder is well distributed with no clumps.
In a medium bowl, whisk together all wet ingredients until smooth: yogurt, eggs, milk, melted oil, honey, and vanilla. The mixture should be completely combined with no streaks of yogurt.
Pour wet ingredients into dry ingredients. Using a spatula or wooden spoon, gently fold together until just combined. The batter will be thick—thicker than regular muffin batter. This is normal. Don't overmix; a few small lumps are fine. If the batter seems dry and crumbly rather than thick but scoopable, add 1-2 tablespoons more milk.
Gently fold in your chosen mix-ins. Distribute evenly through the batter.
Divide batter evenly among the 12 muffin cups, filling each about ¾ full. The batter won't spread much during baking, so you can fill them generously.
Bake for 18-22 minutes. Because of the protein powder, these bake faster than regular muffins. Start checking at 18 minutes. They're done when a toothpick inserted in the center comes out with just a few moist crumbs (not wet batter). The tops should be golden and spring back lightly when touched. Do not overbake—it's better to slightly underbake than overbake protein muffins.
Remove from oven and let cool in the pan for 5 minutes, then transfer to a wire rack. The muffins will firm up as they cool. When they first come out, they might seem too soft—that's okay.
Store cooled muffins in an airtight container in the refrigerator for up to 5 days, or freeze individually wrapped for up to 3 months. Thaw overnight in the fridge or microwave for 30-45 seconds from frozen.
