Preheat your oven to 375 degrees F. Lightly coat a 9×13 baking dish with nonstick spray. Set aside.
Heat the olive oil in a large, deep skillet over medium. Once the oil is hot, add the onion and cook until beginning to soften, 2 to 3 minutes.
Stir in the squash, garlic, chipotle chili powder, cumin, salt, and pepper. Sauté until the squash is softened but still has a bit of chew, about 6 to 8 minutes, stirring occasionally. Taste a few pieces of the squash to make sure it’s the right texture overall. Stir in the beans, cooking just to warm through, about 30 seconds. Remove from the heat.
Spread a thin layer of the enchilada sauce into the bottom of the prepared baking dish. Fill the tortillas with a heaping 1/2 cup of the squash and bean filling, roll snugly, then arrange side by side in the dish, seam-side down. Pour the remaining sauce over the top, then sprinkle the top with cheese.
Bake for 20 to 25 minutes, until hot and bubbly. Let cool slightly, then serve with desired toppings.
TO MAKE VEGAN: Omit the cheese or use a non-dairy cheese alternative.
TO MAKE GLUTEN FREE: Use certified gluten-free corn tortillas. Since corn tortillas are smaller, you are likely to have more enchiladas.
TO MAKE AHEAD: Enchiladas can be assembled and stored unbaked in the refrigerator for up to 1 day or frozen for up to 3 months (let thaw overnight in the refrigerator). Top with red sauce right before baking (do not top, then refrigerate or freeze unbaked, or the enchiladas will become soggy).
TO STORE: Refrigerate baked enchiladas in an airtight storage container for up to 5 days.
TO REHEAT: Rewarm leftovers in a baking dish in the oven at 350 degrees F or in the microwave.
TO FREEZE: Freeze enchiladas in an airtight freezer-safe storage container for up to 3 months. Let thaw overnight in the refrigerator before reheating.