Preheat and prep: Heat the oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or lightly grease with oil.
Mix the dry ingredients: In a large bowl, whisk 1 cup whole-wheat pastry flour, 3/4 cup all-purpose flour (or use 1 3/4 cups whole-wheat pastry total), 1 1/2 teaspoons baking powder, 1/2 teaspoon baking soda, 1 1/2 teaspoons ground cinnamon, 1/2 teaspoon ground ginger, 1/4 teaspoon nutmeg, and 1/2 teaspoon salt.
Whisk the wet ingredients: In a separate bowl, whisk 1 cup pumpkin puree, 2 large eggs, 1/3 cup maple syrup, 1/4 cup light brown sugar, 1/3 cup Greek yogurt (or applesauce), 1/4 cup olive oil, and 1 1/2 teaspoons vanilla extract until smooth.
Combine gently: Pour the wet mixture into the dry ingredients.
Stir with a spatula until just combined. The batter should be thick but scoopable. Do not overmix.
Add mix-ins (optional): Fold in up to 1/2 cup dark chocolate chips, chopped nuts, or pumpkin seeds.
Fill the tins: Divide the batter evenly among the 12 cups, filling each about 3/4 full. For a bakery-style dome, you can slightly mound the centers.
Bake: Bake for 18–22 minutes, until the tops spring back when lightly pressed and a toothpick comes out with just a few moist crumbs.
Cool: Let muffins cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.
This helps set the crumb and prevents sogginess.