Preheat oven to 400°F (200°C). Cut the butternut squash in half lengthwise and scoop out the seeds.
Brush the squash halves with olive oil, sprinkle with half of the salt and pepper, and place cut-side down on a baking sheet. Bake for 40-45 minutes until tender.
While the squash bakes, heat a large skillet over medium heat. Add the diced onion and minced garlic, sautéing until soft (about 5 minutes).
Add the ground beef to the skillet. Cook, crumbling the meat, until browned and cooked through. Drain any excess fat and season with the remaining salt and pepper.
Remove the squash from the oven and carefully flip them over. Fill the cavity of each squash boat with the cooked beef mixture.
Top each stuffed squash evenly with the shredded cheese. Return to the oven and bake for an additional 5-7 minutes, until the cheese is melted and bubbly.
Garnish with chopped fresh parsley before serving.