Heat the olive oil in a large skillet over medium-high heat until shimmering.
Add the diced onion and sliced poblanos and cook, stirring occasionally, until the onion is caramelized and peppers are softened, about 10 minutes.
Add the minced garlic and seeded jalapeños and cook 1 minute until fragrant.
Stir in the ground cumin, kosher salt and pepper, and the quinoa; cook, stirring, for 2 minutes to toast the quinoa slightly.
Pour in 2 cups water, bring to a boil, then cover and reduce heat to low; simmer until quinoa is fluffy and water is absorbed, about 20 minutes.
Remove the skillet from heat and stir in 1 cup enchilada sauce, the drained black beans, chopped cilantro, lime juice, and 1/2 cup shredded cheddar; mix to combine.
Preheat the oven to 350°F (175°C). Pour 1/2 cup enchilada sauce into the bottom of a 9x13 inch baking dish and spread to coat.
Wrap the tortillas in a damp towel and warm in the microwave for about 1 minute to make them pliable.
Spoon a portion of the quinoa and bean filling down the center of each tortilla, tuck the sides and roll, placing each seam-side down in the prepared baking dish.
Pour the remaining enchilada sauce over the rolled tortillas and sprinkle with the remaining shredded cheddar and the shredded pepper jack.
Bake for 15–20 minutes, until the cheese is melted and the sauce is bubbling.
Remove from the oven and top with sliced avocado, a dollop of yogurt, pomegranate arils, and extra cilantro; serve with lime wedges.
