Preheat oven to 375 degrees Fahrenheit (190 degrees Celsius). Line a 12-cup muffin tin with paper liners or grease thoroughly.
In a blender, combine cottage cheese, eggs, melted butter, vanilla, and sugar. Blend for 30-60 seconds until completely smooth.
In a large bowl, whisk together flour, baking powder, baking soda, salt, and cinnamon.
Pour the blended wet ingredients into the dry ingredients. Fold gently with a spatula until just combined. A few lumps are fine.
Gently fold in the drained pineapple and coconut flakes, distributing evenly throughout the batter.
Divide batter evenly among muffin cups, filling each about two-thirds full.
Bake for 18-22 minutes, rotating the pan halfway through, until tops are golden brown and a toothpick inserted in the center comes out clean.
Cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.
Store in an airtight container at room temperature for up to 2 days, refrigerate for up to 5 days, or freeze for up to 3 months.