Peel the beets and slice the beets into 1/2 inch thick rounds, or in wedges. In a medium bowl, toss the beets with olive oil, salt, thyme, and pepper. Place on a baking sheet lined with parchment paper and roast until tender and slightly caramelized, about 20-25 minutes.
In the meantime, whisk together olive oil, shallots, lemon juice, salt, zest, and pepper. Toss prepped apples into the vinaigrette so they do not brown.
Let the beets slightly cool and toss the beets with apples and dressing. Serve and enjoy!