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Special equipment: a 9-by-13-inch baking dish
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Preheat the oven to 350 degrees F.
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For the sauce: Heat the oil in a large skillet over medium heat.
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Add the onions, and cook, stirring frequently, until soft and translucent, about 5 minutes.
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Add the garlic, chile powder, cumin and cayenne, and continue to cook, stirring, until the spices are toasted, about 1 minute.
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Add 2 cups water, the tomato puree and 1/2 teaspoon salt, and bring to a simmer.
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Continue cooking until the sauce reduces and thickens slightly (it should be looser and thinner than marinara sauce), 15 to 20 minutes.
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Set aside to cool slightly.
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For the filling: Squeeze all the excess moisture out of the spinach.
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Put it into a large bowl with the pinto beans, and squeeze with your hands to combine and smash up the beans a little.
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Add half of both the Cheddar and the pepper Jack, half of both the sour cream and the scallions and 1 1/4 teaspoons salt, and stir to combine.
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Spread about 1/2 cup of the tomato sauce in the bottom of a 9-by-13-inch baking dish.
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Lay the tortillas out on a work surface, and spread 1 side of each with about 1 teaspoon of tomato sauce.
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Put about 1/4 cup of the filling across the middle of each tortilla.
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Roll each up, then shingle them in 2 even rows in the baking dish.
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Pour the remaining sauce over the top of the rolled tortillas, and sprinkle with the remaining cheeses.
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Cover the baking dish loosely with foil, and bake until the cheeses are melted and the filling is hot, about 30 minutes.
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Uncover, and continue baking to heat completely through, about 10 minutes more.
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For the topping: Whisk together the remaining sour cream, the lime juice and a pinch of salt in a small bowl.
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Drizzle the mixture over the baked enchiladas, and sprinkle with the remaining scallions.