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Step 1
To make the salsa, heat a large saucepan over medium-high until water flicked into it sizzles, about 2 minutes. Place the tomatoes, serrano, garlic, onion pieces and guajillo chili in the pan; cook, turning the ingredients, until spottily charred, 3 to 5 minutes. If the guajillo chili toasts too quickly, remove the halves as they are done. Let cool for a few minutes off heat.
Step 2
Carefully add 1 cup water to the pan. Add ½ teaspoon salt and the guajillo halves, if removed. Bring to a simmer, then cover, reduce to medium-low and cook, occasionally stirring, until the guajillo is fully softened, 10 to 15 minutes. Transfer the mixture to a blender, add the oregano and let cool for 5 minutes; reserve the pan.
Step 3
Blend on high until smooth, about 1 minute. In the same saucepan over medium, heat the oil until shimmering. Carefully add the puree and bring to a simmer. Cook, stirring occasionally, until the foaminess has dissipated and the sauce is slightly thickened, 6 to 8 minutes. Off heat, taste and season with salt and pepper; you will have about 1¾ cups salsa. Cover to keep warm while you make the enchiladas.
Step 4
To make the enchiladas, heat the oven to 375°F with a rack in the middle position. In a small bowl, stir together the onion, vinegar and ¼ teaspoon salt; set aside. Brush both sides of the tortillas with oil, then arrange them on a rimmed baking sheet (overlapping slightly is fine). Cover tightly with foil and warm in the oven until pliable, about 4 minutes. Remove from the oven; leave the oven on.
Step 5
Lay 4 tortillas on a cutting board; keep the remaining tortillas covered. Distribute 2 tablespoons Chihuahua cheese across the center of each. Sprinkle with 1½ tablespoons queso fresco, then scatter on a generous 1 teaspoon pickled onion. Roll up the tortillas and place seam side down in row down the center of a 9-by-13-inch baking dish. Repeat with the remaining tortillas, cheeses and pickled onion.
Step 6
Cover with the foil used to cover the tortillas. Bake until heated through, 5 to 8 minutes. Meanwhile, if needed, rewarm the salsa, covered and stirring, over medium-low. Remove the baking dish from the oven. Uncover and spoon the salsa onto the enchiladas. Sprinkle with chopped onion, additional queso fresco and cilantro.