Preheat the oven to 350 degrees C. Line 12 muffin cups with paper muffin liners
Combine flour, sugar, 3/4 cup chocolate chips, cocoa powder, and baking soda in a large bowl.
Whisk yogurt, milk, oil, egg, and vanilla in separate bowl until smooth. Pour yogurt mixture into the 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 the preheated oven until a toothpick inserted in the center comes out clean, about 20 minutes.
Cool in the pans for 10 minutes before removing to cool completely on a wire rack.