Prepare Mexican quinoa according to instructions in this recipe. Add to a large mixing bowl and set aside.
Heat a skillet over medium heat and add the onions. Saute until onions have started to soften, about 1 - 2 minutes and add the ground beef. Cook beef until browned, breaking it apart with a wooden spoon as it's cooking, about 5 minutes. Season with salt and pepper.
While beef is cooking, prepare the peppers. Cut the tops off the peppers using a small knife and remove the stem and seeds. Reach inside and pull out any white bits that might remain. If the peppers are not standing up on their own, slice a very small amount off the bottom to even it off (you don't want the bottoms to have holes in them, so slice as little off as possible).
When beef is done cooking, remove it from the pan using a slotted spoon and add this to the mixing bowl with the quinoa. Add cheese and stir everything to combine.
Completely fill each pepper with this mixture and add them to the crockpot, with the peppers standing upright. Pour broth into the pot, being careful not to pour it on the peppers.
Cover and cook on high for 4 hours (or low for 6 - 8).
When ready to serve, remove top and let cool for 5 - 10 minutes. Transfer peppers to plates using a slotted spoon and garnish with desired toppings.