Preheat your oven to 350 degrees F and line a 12-cup muffin tin with liners. Spray the inside of the liners with nonstick cooking spray to prevent sticking.
In a large bowl, mix together the mashed bananas, brown sugar, eggs, almond milk, and vanilla extract. Stir until well combined and smooth.
In another bowl, whisk together the dry ingredients: flour, baking powder, baking soda, cinnamon, and salt. This ensures even distribution of the leavening agents.
Gently fold the dry ingredients into the wet mixture using a wooden spoon. Be careful not to overmix; you want it just combined.
Stir in the melted coconut oil until just incorporated. This adds rich moisture to the muffins.
Transfer half of the batter (about 2 cups) to a separate medium bowl. To this bowl, add the cocoa powder and half of the chocolate chips. Mix until just combined.
To fill the muffin liners, first spoon 1 tablespoon of the plain banana batter into each liner. Then, add 1 tablespoon of the chocolate batter on top. Repeat this until the muffin batter is used up. It’s okay if the batter reaches the top of the liners; they will rise beautifully!
With a knife, lightly swirl the two batters together in each liner. A gentle figure-8 pattern works well; don’t overdo it or the swirls will blend too much.
Gently shake the muffin pan back and forth a couple of times. This helps even out the batter before baking.
Evenly sprinkle the remaining chocolate chips on top of the muffins for a delightful finish.
Bake in the preheated oven for 18 to 25 minutes. Check for doneness by inserting a toothpick; it should come out clean.
Allow the muffins to cool in the pan for 10 minutes, then transfer them to a wire rack to finish cooling. Sprinkle a little flaky sea salt on top before serving for an added touch of flavor.