Preheat an oven. Pat the cod filets dry on all sides with paper towels, then season on all sides with Kosher salt and freshly ground black pepper. Set aside to come to room temperature.
Heat olive oil in a large skillet over medium-high heat. When hot, add diced onion. Season with Kosher salt then cook, stirring occasionally until softened. Add grated garlic, fennel seeds, and crushed red pepper flakes, then cook.
Add cherry tomatoes, season with ½ tsp Kosher salt, then cook, stirring occasionally, until the tomatoes begin to burst. Add in butter beans (along with the liquid) and stir well.
In a mixing bowl, whisk together seasoned breadcrumbs, grated Parmesan, chopped oregano, fresh lemon zest, and a generous pinch of Kosher salt. Stir in extra virgin olive oil, until the breadcrumb mixture is moistened.
Transfer to a preheated oven and cook until the cook is fully cooked through. Garnish with additional fresh oregano and a pinch of flaky sea salt, then serve with lemon wedges. Enjoy!