Preheat oven to 350 degrees F. Line a muffin tin with silicone muffin liners or paper liners then spray with oil spray.
Finely shred carrots. In a large mixing bowl, whisk together carrot, eggs, maple sugar, milk, butter, and vanilla extract. Then add baking flour, baking soda and powder, and salt then mix until combined. Use an ice cream scoop to scoop out the batter halfway full into 18 muffins.
In another bowl or stand mixer, add all ingredients for the cheesecake and beat together for 1-2 minutes until combine. Use a spoon to add about 1-2 tablespoons of the cheesecake mixture on top of each muffin, making sure to not fill to the top.
Lastly, mix together the crumb toppings in a small bowl. Sprinkle the crumb topping on top of each muffin, pressing lightly into the cheesecake layer.
Place in the oven to bake for 25 minutes. Cool for about 10 minutes then eat up!