Place squash in a medium sauce pot and cover with water.
Boil squash over medium heat for 20–30 minutes, until soft.
Remove from heat, drain squash, and set aside.
Sauté onion in 1 tablespoon coconut oil in a cast-iron skillet over medium heat for 8–10 minutes, then add the carrots and cook for another 6–9 minutes until soft.
Add the ground beef and continue sautéing until meat is no longer pink, separating it into crumbles while it cooks.
Add the thyme, sea salt, cumin, black and cayenne pepper, peppers, and spinach, and cook another 3–5 minutes.
Transfer the beef and vegetable mixture to a 9" × 13" baking dish and add the mashed squash on top, distributing evenly; heat for just a few minutes at 375°F, and serve warm.