Prep the squash: Heat the oven to 425°F (220°C). Peel the butternut squash, scoop out the seeds, and cut into 1/2-inch cubes.
The smaller the cubes, the faster they roast.
Season generously: Toss squash with olive oil, cumin, chili powder or smoked paprika, cinnamon if using, salt, and pepper. Spread on a baking sheet in a single layer.
Roast until tender: Roast for 20–30 minutes, tossing once, until the edges are browned and the centers are soft. You want caramelized bits for flavor.
Sauté aromatics: In a skillet over medium heat, add a drizzle of oil.
Cook the sliced onion until soft and lightly browned, 6–8 minutes. Stir in garlic and jalapeño for 1 minute. Season with a pinch of salt.
Combine the filling: Add the roasted squash to the skillet with the onions.
Gently mash a few pieces to help the mixture stick together. Stir in cilantro and a squeeze of lime. Taste and adjust seasoning.
Assemble the quesadillas: Warm a clean skillet over medium heat.
Lightly oil it. Place a tortilla in the pan, sprinkle with cheese, add a layer of the squash mixture, then more cheese. Top with a second tortilla.
Cook until crispy: Cook 2–3 minutes per side, pressing gently with a spatula, until tortillas are golden and the cheese is melted.
Transfer to a cutting board.
Repeat and serve: Continue with remaining tortillas and filling. Slice into wedges. Serve with lime wedges, sour cream or yogurt, salsa, and avocado.
Optional add-ins: If using black beans or corn, fold them into the squash mixture before assembling.
For extra tang, sprinkle in crumbled cotija after the cheese.