Preheat and prep: Heat oven to 375°F (190°C). Line a 12-cup muffin tin with paper liners or lightly grease with oil.
Whisk dry ingredients: In a large bowl, whisk 1 cup whole wheat pastry flour, 3/4 cup all-purpose flour, 1/2 cup unsweetened cocoa powder, 1 1/2 teaspoons baking powder, 1/2 teaspoon baking soda, 1/2 teaspoon fine sea salt, and 1 teaspoon espresso powder.
Mix wet ingredients: In a separate bowl, whisk 3/4 cup Greek yogurt, 1/2 cup unsweetened applesauce, 1/2 cup maple syrup or honey, 2 large eggs, 1 teaspoon vanilla extract, 1/3 cup milk, and 2 tablespoons oil until smooth.
Combine gently: Pour the wet mixture into the dry ingredients. Stir with a spatula until just combined.
A few streaks of flour are fine—don’t overmix.
Add the chocolate: Fold in 1/2 to 2/3 cup dark chocolate chips. Save a few to sprinkle on top for a bakery-style look.
Portion the batter: Divide evenly among the 12 muffin cups. The cups should be about 3/4 full.
Sprinkle the reserved chips over the tops.
Bake: Bake for 16–19 minutes. Start checking at 16 minutes. A toothpick inserted in the center should come out with a few moist crumbs but no wet batter.
Cool: Let muffins cool in the pan for 5 minutes, then transfer to a wire rack.
They will firm up as they cool.
Serve: Enjoy warm for melty chocolate pockets, or at room temperature for a cleaner bite. They’re great with a glass of milk or coffee.