Preheat the oven to 400°F (200°C).
Season the chicken thighs with salt and pepper on both sides.
Heat 1 tablespoon olive oil in a large oven-safe skillet over medium-high heat.
Place the chicken thighs skin-side down and cook 5–6 minutes until the skin is golden and crispy, then flip and cook the other side 5–6 minutes. Remove the chicken from the pan and set aside.
Add the diced onion to the same pan and cook 2–3 minutes until softened; add about 1 teaspoon oil if the pan is dry.
Stir in the minced garlic, cumin, paprika, salt, and pepper and sauté for a few seconds until fragrant.
Add the uncooked rice and black beans to the pan and stir to coat with the aromatics.
Pour in the chicken stock (or water) and bring the mixture to a gentle simmer.
Return the chicken thighs to the skillet, placing them on top of the rice, then cover the pan and transfer it to the preheated oven.
Bake for about 20 minutes, until the rice is tender and the chicken is cooked through.
Remove the cover and broil for a few minutes if desired to further crisp and color the chicken skin.
Remove the chicken from the skillet, stir the lime juice and chopped cilantro into the rice, and gently fluff with a fork.
Rearrange the chicken on top of the rice and serve.