Preheat your oven to 400°F (200°C). Line a large baking sheet with parchment paper for easy cleanup.
In a large bowl, combine the olive oil, soy sauce, brown sugar, minced garlic, ground ginger, black pepper, and red pepper flakes. Whisk until well mixed.
Add the chicken thighs to the bowl and toss them in the marinade until fully coated. Let them marinate for at least 15 minutes, or up to 2 hours in the refrigerator for more flavor.
Arrange the marinated chicken thighs on one side of the prepared baking sheet. On the other side, spread out the pineapple chunks, bell pepper slices, and red onion slices.
Drizzle any remaining marinade over the vegetables.
Bake in the preheated oven for 25-30 minutes, or until the chicken is cooked through and reaches an internal temperature of 165°F (75°C).
If desired, broil for an additional 2-3 minutes to caramelize the edges of the chicken and vegetables.
Serve the chicken and vegetables over cooked rice, garnished with chopped green onions.
Adjust seasoning with additional black pepper if needed before serving.