Brown the butter in a small saucepan over medium heat until golden brown and fragrant. Transfer it to a large mixing bowl and let it cool for about 10 minutes.
Blot the pumpkin puree with paper towels to remove as much excess moisture as possible.
Whisk the browned butter, brown sugar, granulated sugar, and honey together until smooth.
Add the egg yolks, pumpkin puree, and vanilla extract. Mix until fully combined.
In a separate bowl, whisk together the bread flour, cinnamon, ginger, nutmeg, cloves, salt, and baking soda.
Gradually fold the dry ingredients into the wet ingredients until no dry flour remains. Do not overmix.
Cover the dough and refrigerate for at least 30 minutes.
Preheat the oven to 350°F (175°C). Line a baking sheet with parchment paper.
Scoop the dough into 1½-tablespoon portions and place them about 2 inches apart on the prepared baking sheet.
Bake for 11–13 minutes, until the edges are set and the centers still look slightly underbaked.
Let the cookies cool on the baking sheet for 5 minutes before transferring them to a wire rack to cool completely.