In a large bowl, combine the sugars, 2 cups of flour, ground espresso, baking powder, baking soda, and salt by stirring with a whisk. Set aside.
In a separate large bowl, whisk together the yogurt, milk, oil, eggs, vanilla, and cooled espresso until well blended.
Add the dry ingredients to the wet and whisk until just combined. Do not overmix. Add the remaining 1 tablespoon of flour to the chocolate chips and stir to coat the chips. Use a rubber spatula to gently fold the chocolate chips into the batter until just incorporated, scraping down the sides and bottom of bowl as you fold.
Fill the lined muffin wells ⅔ full. Bake for 16-20 minutes until the center of each muffin is just set and springs back when touched. Remove muffin pans from oven and transfer to a wire rack to cool for 5 minutes. Carefully remove the muffins from each pan and place on a wire rack to cool slightly - serve warm or at room temperature!
Store leftover muffins at room temperature for up to 3 days or refrigerate for up to 1 week.