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Preheat oven to 400 F. Place tortillas on a baking sheet, lightly spray with cooking spray and prick all over with a fork.
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Bake for 5-6 minutes, until they are puffed and begin to turn golden.
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Remove from oven and allow to cool.
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In a large skillet, heat the olive oil over medium heat.
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Add the sliced onions to the skillet, season with salt and pepper to taste, and cook over medium-low heat, stirring occasionally, until onions turn translucent.
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Add sweet bell pepper, zucchini, yellow squash, and mushrooms and cool over medium heat for about 5 minutes, or until just tender.
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Remove vegetables from pan.
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Mix enchilada sauce and chipotle chiles,.
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Spoon about 1-2 tablespoons of enchilada sauce over the baked tortillas.
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Top with cheese.
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Place back in the oven and cook for 5-6 more minutes, until the cheese has melted. Remove from oven and garnish with fresh cilantro.