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Preheat your oven to 400 F.
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On a cookie sheet or other baking pan, toss butternut squash with olive oil and season with salt and pepper. Let roast in the oven until soft, about thirty minutes.
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While that cooks, make the sauce. In a large skillet over medium heat warm olive oil and then add onion and peppers. Cook, stirring occasionally, about 5 minutes.
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Add the minced garlic and cook for one minute. Sprinkle in flour, cumin and chipotle peppers. Stir to coat the onion/pepper mixture.
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Whisk in the broth and simmer over medium heat until the sauce has thickened. (I use my immersion blender to combine it a little better, because I was too lazy to mince up my chipotle peppers, but no need to do so if you are less lazy). Season with 3/4 teaspoon kosher salt and 1/4 teaspoon black pepper, taste and adjust seasonings.
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In a bowl, mix roasted squash, beans and 1 cup of the sauce.
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Spread 1/4 cup of the sauce in the bottom of a 8x8 pan.
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Spoon about 1/4-1/3 a cup of the squash/bean/sauce filling into the middle of a tortilla. Roll it shut and place it seam side down in the pan. Repeat with remaining 5 tortillas.
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Spread the rest of the sauce on top of the enchiladas and top with the grated cheese.
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Bake, uncovered, at 400 for 20 minutes or until the cheese has melted and bubbly.
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Serve with sour cream.