Preheat the oven to 400 degrees. Place the beets on a baking sheet, drizzle with 1 tablespoon olive oil, and season with salt and pepper. Roast for 35 to 40 minutes until tender when pierced with a knife. Let cool slightly, then peel off the skins.
Add the feta cheese, 2 tablespoons olive oil, garlic clove, and lemon juice to a food processor. Blend until smooth and creamy, scraping down the sides as needed.
Cut the roasted beets into chunks and add them to the food processor. Pulse until the beets are fully incorporated and the dip turns a uniform pink color. Taste and add salt or pepper if needed.
Arrange the baguette slices on the same baking sheet and toast in the oven for 8 to 10 minutes until golden and crisp.
Transfer the dip to a serving bowl, sprinkle with fresh thyme leaves, and serve with the toasted crostini.