Preheat oven to 325 degrees Fahrenheit (165 degrees Celsius) and line a 12-cup muffin tin with paper or silicone liners.
Process the cottage cheese in a high-speed blender or food processor until the texture is completely smooth and creamy.
Add the softened cream cheese, Greek yogurt, maple syrup, eggs, and vanilla extract to the blender and pulse until the mixture is homogenous.
Transfer the liquid base to a mixing bowl and fold in the grated carrots, chopped walnuts, cinnamon, ginger, salt, and coconut flour until evenly distributed.
Divide the batter equally among the prepared muffin liners, filling each approximately three-quarters full.
Bake for 22 to 25 minutes or until the edges are firm and the centers have a slight jiggle.
Remove from the oven and allow the cups to cool at room temperature for 30 minutes.
Refrigerate the cheesecake cups for a minimum of 3 hours to allow the protein structure to set fully before serving.