- Thoroughly rinse fresh produce under warm running water for 20 seconds. Scrub to remove excess dirt.
- Preheat oven to 400 degrees. Line a baking sheet with parchment paper.
- Toss squash, carrot, and sweet potato with 1 teaspoon olive oil, thyme, and a generous pinch of salt. Spread in a single layer on the prepared baking sheet. Bake for 30 minutes, then turn the vegetables and add shallots to the sheet. Bake for an additional 15 minutes.
- While vegetables are cooking, whisk together remaining 3 tablespoons olive oil, lemon juice, and salt and pepper to taste in a large bowl. Stir in pumpkin seeds and cooked quinoa.
- When vegetables are tender, let cool slightly, then add to quinoa mixture and stir to combine.