Preheat oven to 325°F (165°C). Line a baking sheet with parchment paper.
Rinse pumpkin seeds under cool water if dusty. Pat dry thoroughly with a clean towel.
In a medium mixing bowl, stir together melted butter and vanilla extract.
Add pumpkin seeds to the bowl and toss until evenly coated.
In a small bowl, combine ground coffee, granulated sugar, brown sugar, cinnamon, nutmeg, and sea salt.
Pour the coffee-spice mixture over the seeds. Stir until every seed is coated.
Spread seeds in a single layer on the prepared baking sheet.
Bake for 25–30 minutes, stirring halfway through to prevent burning.
Check during the last 5 minutes. Seeds should be golden brown and fragrant.
Remove from the oven and let cool completely. The flavor deepens as they cool.