Preheat the oven to 300 degrees F. Line a baking sheet with parchment paper.
Toss the pumpkin seeds in a bowl with the olive oil and lime juice until well coated. In a separate small bowl, stir together the lime zest, parsley, thyme, chipotle powder and salt. Sprinkle the mixture over the pumpkin seeds and toss to coat evenly. Spread the seeds in a single layer on the prepared baking sheet.
Bake, stirring the seeds halfway through and rotating the baking sheet, until golden brown, about 20 minutes. Serve warm or at room temperature.