Toss the beets in a bowl with the olive oil, vinegar and thyme; season with salt and pepper. Lay the beets cut-side down on a baking sheet. Roast until the beets are slightly tender and a little crispy on the edges, 35 to 40 minutes.
Meanwhile, combine the cocoa powder, chile powder and paprika in a small bowl. Season the steak with salt and pepper, then rub with the cocoa mixture.
Heat a heavy-bottomed ovenproof saute pan or cast-iron skillet over medium-high heat. Add the canola oil and heat until it begins to smoke. Add the steak and sear on one side until heavily caramelized, 6 to 7 minutes. Flip the steak, transfer the pan to the oven and roast until the internal temperature reaches 125 degrees F for medium rare, about 10 minutes. Allow the steak to rest for 15 minutes before slicing. Serve with the roasted beets.