Preheat oven to 425°F. Line a 12-cup muffin pan with paper liners; lightly coat the liners with baking spray.
Whisk ¾ cup all-purpose flour, ¾ cup whole-wheat flour, ¼ cup cocoa powder, 2 teaspoons espresso powder, 1 teaspoon baking powder, 1 teaspoon baking soda and ¼ teaspoon salt in a large bowl until combined.
In a separate large bowl, whisk 1 cup banana, ⅔ cup yogurt, ½ cup almond butter, 5 tablespoons honey, ¼ cup milk, 2 tablespoons oil, 1½ teaspoons vanilla and 1 egg until smooth.
Fold the banana mixture into the flour mixture just until a few streaks of flour remain. Fold in ½ cup pecans just until incorporated. Do not overmix.
Spoon a generous ⅓ cup batter into each prepared muffin cup, spreading evenly. (The liners will be filled to the top.)
Bake for 5 minutes. Reduce the oven temperature to 350°F and continue baking until a wooden pick inserted in the center comes out mostly clean with a few moist crumbs, about 12 minutes.
Let cool in the pan for 5 minutes, then transfer to a wire rack. Serve warm or at room temperature.
To freeze: Wrap the completely cooled muffins individually in plastic wrap or foil. Arrange in a single layer in a large sealable freezer bag, pressing out as much air as possible. Freeze for up to 1 month.
To serve at room temperature: Let frozen muffin(s) stand at room temperature until thawed, about 2 hours.
To reheat (microwave): Unwrap 1 frozen muffin and place on a microwave-safe plate. Cover with a damp paper towel. Microwave on Medium (50% power) in 10- to 15-second intervals until warmed through, 30 to 45 seconds.
To reheat (oven): Unwrap 1 frozen muffin and wrap loosely in foil, if desired. Bake in a 350°F oven until warmed through, 12 to 15 minutes.
