Heat olive oil in a large oven-safe skillet over medium-high heat. Add the diced onion and minced garlic, sautéing for 2-3 minutes until soft.
Add the ground beef to the skillet, breaking it apart with a spatula. Cook for 5-7 minutes until completely browned with no pink remaining. Drain any excess grease.
Stir in the cubed butternut squash, cumin, chili powder, and salt. Pour in the red enchilada sauce and stir to combine. Bring to a gentle simmer, reduce the heat to low, cover, and cook for 12-15 minutes until the squash is fork-tender.
Remove the lid and stir in the black beans. Cook for an additional 2 minutes until the beans are heated through.
Sprinkle the shredded cheese evenly over the top of the mixture. Transfer the skillet to the broiler for 2-3 minutes, or until the cheese is completely melted and lightly bubbly.
Remove from the oven, garnish with fresh chopped cilantro, and serve immediately.