Preheat oven to 400 degrees Fahrenheit.
Spray mini muffin pans with cooking spray. (Alternatively, you could use butter or coconut oil to grease each muffin tin.)
Whisk together the flour through nutmeg in a medium bowl.
In another, larger bowl, mix together the brown sugar, maple syrup, oil, and eggs. Whisk well to combine. Add the pumpkin and vanilla and whisk.
Add half of the flour mixture to the sugar-pumpkin batter. Whisk until combined and then add the cultured milk and the rest of the flour. Mix until just combined.
Using a spoon or a small scooper, scoop the batter into the muffin pan. Add a chocolate chip, pecan, or a few pumpkin seeds to the tops of each muffin, pressing them in slightly with your fingers.
Bake for 10-12 minutes or until lightly browned and a toothpick inserted into the middle comes out clean.
Cool on a wire rack and enjoy!