Preheat your oven to 375 degrees F. Lightly coat a 9x13 baking dish with cooking 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, 2-3 minutes. Stir in the squash, garlic, sage, 3/4 teaspoon salt, pepper, and 1/4 teaspoon nutmeg.
Cover and let cook until the squash is softened but still has a bit of chew, about 6-8 minutes, stirring occasionally.
Stir in the drained beans and spinach. Remove from heat, then toss with 1/2 cup of the grated cheese. Set aside.
Meanwhile, melt the butter in a large saucepan over medium-high. Sprinkle in the flour, then whisk for 2-3 minutes, until the flour turns golden and smells nutty. Slowly pour in about 1/2 cup of the almond milk, whisking constantly until the flour is smooth. Add the rest of the milk, then let the mixture bubble, stirring occasionally, until it thickens, about 5 minutes. Remove from the heat and stir in the remaining 1/4 teaspoon nutmeg, remaining 1/4 teaspoon salt, and 1/2 cup grated cheese.
Pour a thin layer of the cheese sauce into the bottom of the prepared baking dish. Fill the tortillas with the squash and bean filling, roll snugly, then arrange side by side in the dish. Pour the remaining white sauce over the top, then sprinkle the top with the remaining 1/2 cup cheese.
Bake for 20-25 minutes, until hot and bubbly. Let cool slightly, then serve.
*VEGANOPTION: To make the recipe vegan and dairy-free, use a dairy-free mozzarella-style shredded cheese alternative. Also, check the ingredients of your tortillas to confirm they do not contain lard.
TO STORE: Keep leftover enchiladas in an airtight container in the fridge for up to 3 days.
TO REHEAT: Gently warm enchiladas on a baking sheet in the oven at 350 degrees F until heated through. You can also rewarm this recipe in the microwave.
TO FREEZE: Assemble, as directed, without the sauce and cheese on top. Then cover and freeze for up to 3 months. When ready to bake, prepare the sauce and then top the frozen enchiladas with sauce and cheese. Bake as directed for an extra 30-40 minutes (55-65 minutes total).
TO MAKE-AHEAD: Prepare the filling and sauce, as directed, a full day ahead. Store overnight in airtight containers, then assemble the enchiladas the next day. Note the cheese sauce will thicken in the fridge. I recommend gently warming it on the stove (or microwave on low) with a bit of extra milk prior to assembling. Bake as directed.