Chop the veggies: cut the carrots into 2 inch pieces. Slice the potatoes into rounds then in half. Cut the acorn squash in half then slice into 2 inch pieces. Slice the shallots into quarters.
Add the chopped vegetables to a large bowl and season with the olive oil and spices. Toss well to combine. Transfer the seasoned veggies to a large baking dish.
Prepare the honey chipotle walnuts by tossing the walnuts with the honey, olive oil, thyme and chipotle powder. Spread the glazed walnuts over the veggies.
Cover the dish and bake for 30-40 minutes, then uncover and bake for another 30-35. Bake time will vary depending on your oven and baking dish used. The vegetables should be fork tender when uncovering.
Garnish with extra thyme and flakey sea salt before serving