Season halibut fillets with salt and black pepper on all sides.
In a large skillet over medium-high heat, heat the olive oil until shimmering. Add halibut and sauté until golden brown on one side, about 3 to 5 minutes.
Flip filets and continue to sauté until cooked through, about 3 to 5 minutes longer (halibut should register 145 degrees in the thickest part of the filet on a digital thermometer). Transfer filets to a plate and loosely tent with aluminum foil to keep warm.
Return the pan to medium-high heat, add onion and sauté 1 minute. Add bell peppers and continue to sauté until the vegetables are softened, about 3 to 5 minutes.
Add the diced tomatoes, olives, and thyme, then add lemon juice and stir or whisk to pull up any browned bits and fond from the bottom of the pan. Simmer until the flavors have blended, about 2 minutes longer. Season to taste with salt and black pepper.