Preheat the oven. Set to 400°F (200°C).
Line a baking sheet or a large baking dish with parchment for easy cleanup.
Prepare the zucchini boats. Trim the ends, slice each zucchini lengthwise, and use a spoon to scoop out the center, leaving about 1/4 inch border. Reserve roughly half the scooped flesh and chop it finely.
Season and par-bake the shells. Brush the zucchini halves with 1 tablespoon olive oil, season with salt and pepper, and place cut side up. Bake for 10–12 minutes until slightly tender but still holding shape.
Build the filling base. In a skillet, warm 2 tablespoons olive oil over medium heat.
Add red onion and cook 3–4 minutes until translucent. Stir in garlic and the chopped zucchini flesh; cook 2 more minutes.
Add the veggies and spices. Stir in tomatoes, oregano, cumin, and red pepper flakes. Cook 2–3 minutes until tomatoes soften and release juices.
Fold in grains and protein. Add cooked quinoa or couscous and chickpeas.
Season with salt and pepper. Warm through for 1–2 minutes so the flavors meld.
Finish with Mediterranean flair. Off the heat, add olives, feta, parsley, mint or basil, lemon zest, and lemon juice. Taste and adjust seasoning.
Stir in pine nuts if using.
Stuff the boats. Spoon the filling into the par-baked zucchini, mounding it slightly. Top with a little extra feta if you like.
Bake to finish. Return to the oven for 12–15 minutes, until the zucchini is tender and the filling is hot and lightly golden on top.
Make the optional yogurt sauce. Stir together Greek yogurt, lemon juice, olive oil, and a pinch of salt. Thin with a splash of water if needed.
Serve. Drizzle with yogurt sauce or a squeeze of lemon.
Finish with a sprinkle of parsley and a crack of black pepper.