Preheat the oven to 325 degrees F (165 degrees C). Coat 2 muffin tins with cooking spray.

Whisk pumpkin puree, eggs, sugar, water, applesauce, MCT oil, stevia, and vanilla extract together in a large bowl.

Stir flour, protein powder, ground pecans, flaxseed meal, baking soda, salt, cinnamon, nutmeg, cloves, and ginger together in a separate bowl. Pour over pumpkin mixture and mix until batter is just moistened.

Scoop batter into the prepared tins, filling each cup 2/3 full.

Bake in the preheated oven until a toothpick inserted into the center comes out clean, 15 to 17 minutes.