Preheat your oven to 400°F (200°C). Line a large baking sheet with parchment paper for easy cleanup.
In a large bowl, whisk together soy sauce, honey, olive oil, rice vinegar, minced garlic, ground ginger, salt, and pepper.
Add the chicken thighs to the bowl and toss to coat them evenly with the marinade. Let it marinate for at least 15 minutes (or up to 2 hours in the refrigerator for more flavor).
Arrange the marinated chicken thighs on the prepared baking sheet. Scatter the pineapple chunks, red and yellow bell peppers, and red onion around the chicken.
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).
Broil on high for an additional 2-3 minutes to caramelize the edges, if desired.
Remove from the oven and let it rest for 5 minutes. Garnish with chopped green onions before serving.