Heat your oven to 375 degrees. Grease a large rimmed baking sheet with cooking spray or line it with parchment paper.

In a large bowl, whisk together the flour, baking soda, baking powder, salt, cinnamon, nutmeg, ginger, and cloves until evenly combined. Set aside.

In a medium bowl, whisk the brown sugar and oil together until smooth. Add the eggs one at a time, whisking after each. Stir in the pumpkin puree and vanilla until the mixture looks uniform and a bit glossy.

Pour the wet ingredients into the dry ingredients and fold with a rubber spatula until just combined. A few small streaks of flour are fine. Fold in 1 cup of the chocolate chips. Do not overmix or the muffin tops will come out tough.

Scoop the batter onto the prepared pan using a large cookie scoop or a heaping tablespoon, spacing each mound about 2 inches apart. You should get about 14 mounds. Gently press each one down with your fingertips just enough to flatten the peak so the top is even, not pointed. Scatter the remaining 1/4 cup of chocolate chips on top of each one.

Bake for 11 to 13 minutes. The edges should look just set and lightly golden, but the centers will still look soft. That is correct. They finish cooking on the hot pan as they cool. If you bake until the center looks fully done, the edges will overbrown.

Let them cool on the pan for 5 minutes before transferring to a wire rack. They are best warm but hold their texture well at room temperature.