Preheat the oven to 350°F (175°C) and grease a 12-cup muffin pan with nonstick spray.
Make a flax egg: combine the ground flaxseed and water in a small bowl and let sit until thickened, about 5 minutes.
In a large bowl, whisk together the oats, baking powder, sea salt, and cinnamon.
In a medium bowl, mash the ripe banana, then stir in the flax mixture, melted coconut oil, milk, brown sugar, and vanilla until smooth.
Pour the wet ingredients into the dry ingredients and stir until just combined, then fold in the mini chocolate chips.
Divide the batter evenly among the prepared muffin cups and smooth the tops.
Bake for 20–25 minutes, until the tops are golden and set in the center.
Let the baked oatmeal cups cool in the pan for 5 minutes, then remove and serve warm.