Prep the oven and pan. Heat the oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or lightly grease with oil spray.
Whisk the dry mix. In a large bowl, whisk the flours, protein powder, ginger, cinnamon, nutmeg, cloves, baking powder, baking soda, and salt. Break up any protein powder clumps.
Stir the wet mix. In a separate bowl, whisk eggs, Greek yogurt, molasses, maple syrup, oil, vanilla, and 1/4 cup milk until smooth.
Combine gently. Pour wet into dry and fold with a spatula just until no dry streaks remain.
If the batter seems very thick (protein powders vary), add 1–2 tablespoons extra milk. It should be scoopable but not runny.
Add extras if you like. Fold in chocolate chips, nuts, or orange zest. Do not overmix.
Fill the cups. Divide batter evenly among the 12 muffin cups, filling each about 3/4 full.
Bake. Bake for 15–18 minutes, or until the tops spring back and a toothpick comes out with a few moist crumbs.
Start checking at 14 minutes if your oven runs hot.
Cool. Let muffins rest in the pan for 5 minutes, then transfer to a wire rack to cool completely. This helps them set and stay moist.
Finish and enjoy. Serve plain or with a smear of almond butter or a dollop of Greek yogurt. The spices deepen by day two.