Preheat your oven to 350°F and generously grease a standard 12-cup muffin tin with butter or cooking spray. This ensures your muffins won't stick and will have nice, even browning on the sides. Having the tin ready before blending your batter saves time and prevents the batter from sitting.
Add the cottage cheese, oats, room temperature eggs, maple syrup, and vanilla to a blender, then add the baking powder, cinnamon, nutmeg, and salt. Blend on medium speed for 30 seconds until the mixture becomes smooth and well-combined—the oats will break down and incorporate fully. I like to use a blender rather than a bowl mixer here because it breaks down the oats more thoroughly, creating a more tender crumb. Don't overblend beyond 30 seconds, as this can overdevelop the batter and make the muffins tough.
Pour the blended batter into a bowl and gently fold in 6 tablespoons of chocolate chips by hand, reserving a small handful for topping if desired. Let the batter rest for 5 minutes at room temperature—this allows the oats to fully hydrate and the baking powder to activate slightly, which helps the muffins rise more evenly in the oven.
Divide the batter evenly among 9 of the greased muffin cups, filling each about three-quarters full. I like to reserve some chocolate chips to sprinkle on top of each muffin before baking—this creates a little texture and sweetness on the surface. Distribute the reserved chips across the tops of the filled muffins.
Place the muffin tin in the preheated 350°F oven and bake for 22 to 25 minutes, until the tops are lightly golden and a toothpick inserted into the center of a muffin comes out clean or with just a few moist crumbs. The exact time depends on your oven, so start checking around the 22-minute mark.
Remove the muffin tin from the oven and let the muffins cool in the tin for 5 minutes, then turn them out onto a wire rack to cool completely. This brief cooling period in the tin allows the muffins to set and hold their shape, while the wire rack prevents them from becoming soggy from trapped steam.