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Heat oven to 425°F (218°C). Prepare a 12-count muffin tin with nonstick spray or line with paper liners.
In a large bowl, whisk together flour, sugar, cocoa powder, baking soda, salt, and chocolate chips. Set aside.
In a separate bowl, whisk eggs, sour cream, oil, milk, and vanilla extract until well combined then whisk in the sourdough discard.
Pour wet ingredients into dry ingredients. Gently fold together using a silicone spatula or wooden spoon until just combined. (The batter will be thick and sticky. Avoid overmixing to help keep the muffins light in texture.)
Divide batter evenly among prepared muffin cups, filling each all the way to the top.
Bake at 425°F for 5 minutes. Without opening the oven door, reduce temperature to 350°F (177°C). Continue baking for 15-16 minutes until a toothpick inserted in the center comes out clean. Total baking time: approximately 20-21 minutes.
Let muffins rest in the pan for 10 minutes, then transfer to a wire rack to cool completely before serving.