Preheat oven to 400 degrees F (200 degrees C). Grease 12 muffin cups or line with paper muffin liners.
Combine flour, sugar, 3/4 cup chocolate chips, cocoa powder, and baking soda in a large bowl. Whisk egg, yogurt, milk, and vegetable oil in another bowl until smooth; pour into chocolate mixture and stir until batter is just blended. Fill prepared muffin cups 3/4 full and sprinkle with remaining 1/4 cup chocolate chips.
Bake in preheated oven until a toothpick inserted into the center comes out clean, about 20 minutes. Cool in the pans for 10 minutes before removing to cool completely on a wire rack.