Season both sides of the chicken thighs with salt and pepper. Heat 1 tablespoon of butter over medium-high heat in a large pot. Place the chicken thighs skin-side down in the pot and cook for 3-4 minutes until browned. Remove the chicken and set it aside on a plate.
Add the remaining 2 tablespoons of butter to the pot and melt. Add the diced onions and sauté for 2-3 minutes until softened.
Stir in the diced red bell pepper, minced garlic, tomato paste, paprika, salt, and black pepper. Continue to cook, stirring frequently, for another 2-3 minutes until fragrant.
Pour in the chicken stock and stir to combine. Reduce the heat to medium. Add the chicken thighs back to the pot, skin-side down, and simmer for 20-25 minutes, turning halfway through cooking.
Once the chicken is cooked through (internal temperature of 165°F), remove the chicken from the pot and set aside.
In a small bowl, whisk together the flour and sour cream. Gradually mix in 1/2 cup of the onion and pepper liquid from the pot into the sour cream mixture until smooth. This will prevent the flour from clumping.
Stir the sour cream mixture back into the pot until well combined and the sauce is thickened.
Return the chicken to the pot, coating it with the sauce.
Garnish with freshly chopped parsley and serve with spaetzle, noodles, or roasted potatoes.