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In a medium bowl, combine the Chili Barbecue Sauce, root beer, and thyme leaves.
Arrange the onions evenly in the bottom of a 9" x 13" pan.
Season the short ribs on all sides with salt and pepper. Lay in a single layer on top of the onions.
Pour the chili-root beer sauce evenly over the ribs. Cover the pan tightly with aluminum foil.
When ready to cook, start the Traeger grill on Smoke with the lid open until the fire is established (4 to 5 minutes). Set the temperature to 300F and preheat, lid closed, for 10 to 15 minutes.
Place the pan of ribs on the grill grate; cook for 2 to 3 hours, or until the ribs are tender but not falling off the bone.
Add a bit more root beer to the pan if the dish does not seem as saucy as you would like.
Serve immediately with polenta or mashed potatoes.