Heat the oven: Preheat to 375°F (190°C). Lightly oil a baking dish large enough to snugly fit the peppers.
Cook the quinoa: In a pot, combine rinsed quinoa and broth.
Bring to a boil, then reduce to a simmer, cover, and cook 15 minutes, or until fluffy. Remove from heat and let stand 5 minutes, covered. Fluff with a fork.
Prep the peppers: Slice off the tops and scoop out seeds and membranes.
Rub the insides with 1 tablespoon olive oil and a pinch of salt. Set them upright in the baking dish. If they wobble, trim a thin slice off the bottoms to level.
Sauté aromatics and veg: Warm 1 tablespoon olive oil in a skillet over medium heat.
Add onion and a pinch of salt; cook 3–4 minutes until translucent. Stir in garlic for 30 seconds. Add zucchini; cook 3–4 minutes until just tender.
Remove from heat.
Mix the filling: In a large bowl, combine quinoa, sautéed vegetables, tomatoes, olives, feta, parsley, mint, oregano, lemon zest, 1–2 tablespoons lemon juice, remaining 1 tablespoon olive oil, and red pepper flakes if using. Season generously with salt and pepper. Taste and adjust acidity or salt to your liking.
Stuff the peppers: Spoon the filling into each pepper, mounding slightly.
If you have extra, tuck it around the peppers in the dish.
Bake: Cover the dish loosely with foil and bake 25 minutes. Uncover, sprinkle a little extra feta on top, and bake another 10–15 minutes, until the peppers are tender and the tops are lightly golden.
Finish and serve: Let rest 5 minutes. Add a squeeze of lemon and a drizzle of olive oil.
Garnish with extra parsley or mint. Serve warm.