Prep the pan: Heat oven to 350°F (175°C). Line a 12-cup muffin tin with liners or lightly grease.
Mix dry ingredients: In a large bowl, whisk flour, baking soda, baking powder, salt, and spices until well combined.
Whisk wet ingredients: Add pumpkin, eggs, maple syrup, oil, yogurt, and vanilla.
Whisk until smooth.
Combine: Add the dry ingredients to the wet. Stir gently with a spatula until just combined. If the batter is very thick, fold in 2–3 tablespoons milk to loosen slightly.
Do not overmix.
Add-ins: Fold in chocolate chips or nuts, if using.
Fill the cups: Divide batter evenly among the muffin cups, filling each about 3/4 full. Sprinkle pepitas on top if you like.
Bake: Bake 18–22 minutes, until the tops spring back and a toothpick comes out clean or with a few moist crumbs.
Cool: Let muffins rest in the pan 5 minutes, then transfer to a wire rack to cool completely. This helps them set and stay moist.