Preheat the oven to 400 degrees F. Toss the cut sweet potatoes and beets with olive oil and season with salt and pepper. Place on a parchment-lined baking sheet and bake until vegetables are golden, about 25 to 30 minutes, stirring every 10 minutes.
Meanwhile, in a medium skillet over medium-low heat, add the bacon and render the fat until the bacon is crispy. Add the onions and season with salt, and continue to cook until the onions start to caramelize and turn golden, about 10 minutes. Add the roasted sweet potatoes and beets to the pan and stir to combine cooking another 5 minutes. Taste and adjust the seasoning, if necessary and serve immediately.