Cover quinoa with vegetable broth in an oven-proof saucepan. Bring to a boil. Cover the saucepan with aluminum foil.
Bake in preheated oven until quinoa is dry and fluffy, about 15 minutes. Keep covered.
Heat a skillet over medium heat. Pour in vegetable oil. Cook and stir onion and garlic until soft, about 5 minutes. Stir in tomatoes, annatto paste, vinegar, paprika, oregano, cumin, and chipotle pepper. Cook until mixture is thick and stew-like, 10 to 15 minutes.
Toss the mixture with the baked quinoa. Let cool, about 10 minutes. Season with salt.