Heat roasting pan or large iron skillet in 400˚ F oven for 5 minutes.
Trim tops of beets and carrots leaving 1-inch stems. Scrub vegetables thoroughly under running water with a vegetable brush. Scrape vegetables with the edge of a knife to remove outer peeling, if desired. Leave vegetables whole or cut larger vegetables into halves or quarters for more even cooking.
Place vegetables in a large bowl. Add shallot and olive oil, tossing to coat. Arrange vegetables in a single layer in hot roasting pan. Bake at 400 for 30 to 40 minutes until vegetables are tender, stirring after 20 minutes. Remove from oven and sprinkle with salt, pepper, and thyme. Garnish with thyme sprigs, if desired.