Bring a large pot of salted water to a boil over high heat.
Meanwhile, heat oil in a large skillet over medium heat. Add onion, bell pepper, and poblano and cook, stirring occasionally, for 5 to 7 minutes or until onions are translucent.
Add garlic and cook for another minute. Stir in cumin, chili powder, thyme, red pepper flakes, salt, tomatoes, and beans. Lower the heat, cover, and simmer for 5 minutes.
When the water is boiling, stir in the pasta and adjust the heat to maintain a low boil. Cool until pasta is al dente (reference package directions).
Combine all the queso ingredients in a high speed blender and process until completely smooth. If the sauce is too thick to pour, add another tablespoon of water.
Fold tomato bean mixture, pasta, and queso together until combined. Top with scallions and season with more salt and pepper (if needed).