Preheat the oven to 350°F (175°C). Line a 12-cup muffin pan with paper liners.
In a medium bowl, whisk together the gluten-free flour, almond flour, chocolate protein powder, cacao powder, baking powder, baking soda, and salt.
In a large bowl, mash the bananas until mostly smooth.
Add the egg, maple syrup, olive oil, and vanilla extract to the mashed bananas. Whisk until combined.
Add the dry ingredients to the wet ingredients and stir until a thick batter forms.
Fold in the dark chocolate chips.
Divide the batter evenly between the prepared muffin cups.
Top with extra chocolate chips and a small pinch of flaky sea salt if desired.
Bake for 16 to 20 minutes, or until the muffins are risen and a toothpick inserted into the center comes out with a few moist crumbs.
Cool in the pan for 5 minutes, then transfer to a cooling rack.