Preheat the oven to 350°F. Line a 6-cup muffin tin with liners and lightly spray them with oil. Foil liners work best.
In a large bowl, whisk the eggs, Greek yogurt, melted butter, stevia, and vanilla.
Mix in the almond flour, followed by the protein powder, and finally, the baking powder. Mix until smooth.
Fold in the chocolate chips, reserving 24 chocolate chips to sprinkle on the muffins.
Spoon the batter into the prepared muffin cups, filling them almost full. Top each muffin with 4 chocolate chips.
Bake until a toothpick inserted in one of the muffins comes out clean, 17-19 minutes. They will not brown much.
Cool the muffins for 5 minutes in the pan on a wire rack and then for 10 more minutes directly on the rack before serving.
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Notes
Foil liners work best in this recipe to prevent sticking. It's best to peel paper liners off while the muffins are still warm. Otherwise, they tend to slightly stick to the muffins. Greased foil liners don't stick.
Protein powder is very drying, so it's best to measure it by weight using a kitchen scale, not by volume.
You can mix the batter the night before, pour it into the muffin pan, cover it with cling wrap, and refrigerate it. Then, bake the muffins in the morning.
You can replace the chocolate chips with ½ cup of blueberries. The blueberries tend to sink to the bottom of the muffins, but the muffins are still delicious. Coating the blueberries in a teaspoon of cornstarch before adding them to the batter helps mitigate some of the sinking but doesn't prevent it.
You can double this recipe and bake 12 muffins. They keep fairly well in the fridge, in an airtight container, for 4-5 days and can be gently warmed up in the microwave. If you made them with blueberries, place them on paper towels to absorb extra liquid. These muffins also freeze well in freezer bags. You can thaw them in the microwave.