First, let’s get those sweet potatoes ready. Prick them all over with a fork and microwave them for about 8-10 minutes, flipping halfway through. You’ll know they’re done when you can easily slide a knife through them like butter.
While the potatoes cool, preheat your oven to 375°F and line a 12-cup muffin tin with paper liners. I like to give the top of the pan a light spritz with cooking spray too, just in case the muffins spill over while baking.
Once the sweet potatoes are cool enough, split them open and scoop out the flesh. Mash it really well with a fork until it’s smooth – any lumps now will show up in your muffins later. Measure out 1½ cups and set aside any extra for another use.
In a large bowl, whisk together mashed sweet potatoes, eggs, oil, milk, and vanilla until everything’s well combined. The mixture should be pretty smooth, though you might see tiny bits of sweet potato – that’s totally fine.
Now, grab a medium bowl for your dry ingredients. Whisk together the flour, sugar, baking powder, cinnamon, salt, and nutmeg until they’re evenly mixed. The cinnamon and nutmeg might try to clump up, so break up any little spice balls you see.
Add the dry ingredients to the wet mixture in two batches, stirring just until you don’t see any more dry flour. The batter will be pretty thick – that’s exactly what you want. Fold in the chocolate chips, making sure they’re evenly distributed.
Divide the batter between the muffin cups – they should be about ¾ full.
Bake for 18-22 minutes, or until a toothpick inserted into the center of a muffin comes out clean (ignore any melted chocolate on the toothpick). The tops should be lightly golden brown and will spring back when you gently press them with your finger.
Let the muffins cool in the pan for about 5 minutes. Then transfer them to a wire rack to cool completely.