Prep the pan and oven. Heat the oven to 350°F (175°C). Line a 12-cup muffin tin with liners or lightly grease with oil spray.
Whisk the wet ingredients. In a large bowl, whisk peanut butter, honey (or maple), Greek yogurt (or banana), eggs, vanilla, and milk until smooth and glossy.
Combine the dry ingredients. In a separate bowl, stir together the flour, baking powder, baking soda, salt, and optional flax or chia.
Bring it together. Add the dry mixture to the wet mixture. Stir gently with a spatula until just combined.
Do not overmix; a few small streaks of flour are fine.
Fold in the chocolate. Add the mini chocolate chips and fold briefly, reserving a tablespoon for the tops if you like.
Fill the cups. Divide the batter evenly among the muffin cups, about 3/4 full. Sprinkle the reserved chips on top.
Bake. Bake for 15–18 minutes, or until the muffins are set, lightly golden, and a toothpick in the center comes out with a few moist crumbs (not wet batter).
Cool. Let the muffins rest in the pan for 5 minutes, then transfer to a rack to cool fully. This helps them set and stay tender.