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Preheat oven to 425°F (218°C). Spray a 12-count muffin pan with nonstick spray or use cupcake liners. This recipe yields about 14 muffins, so prepare a second muffin pan in the same manner or bake in batches and reserve leftover batter at room temperature for when the first batch is done.
Whisk the flour, sugar, cocoa powder, baking soda, salt, and chocolate chips together in a large bowl. Set aside.
Whisk the eggs, sour cream, oil, milk, and vanilla extract together until combined. Pour wet ingredients into dry ingredients and fold together with a rubber spatula or wooden spoon until completely combined. (Batter is quite thick, so I recommend a spatula or spoon over a whisk.) Avoid overmixing. The batter will be thick and sticky.
Spoon the batter into liners, filling them all the way to the top. Bake for 5 minutes at 425°F then, keeping the muffins in the oven, reduce the oven temperature to 350°F (177°C). Bake for an additional 15-16 minutes or until a toothpick inserted in the center comes out clean. The total time these muffins take in the oven is about 20-21 minutes, give or take. (For mini muffins, bake 13-14 total minutes at 350°F (177°C) the whole time.)
Cool muffins for 10 minutes in the pan, then transfer to a wire rack until ready to eat.
Cover leftover muffins and store at room temperature for 5 days or in the refrigerator for 1 week.