In a large 12-inch skillet, heat 2 tbsp olive oil over medium heat. Add onion; cook 5–7 minutes until softened and translucent.
Add red and green bell peppers and zucchini; cook 8–10 minutes, stirring, until tender and lightly browned.
Add garlic, smoked paprika, cumin, coriander, and red pepper flakes; stir constantly for 45 seconds until fragrant, then mix through vegetables.
Add tomatoes with juices, cannellini beans, bay leaf, and black pepper; stir, scraping up browned bits.
Bring to a vigorous simmer, reduce heat to low, cover, and simmer 15 minutes to meld flavors and slightly thicken. If the sauce is thin, uncover and simmer 5–10 minutes more to reduce.
Remove lid and bay leaf. Stir in spinach until wilted. Make six small wells; crack one egg into each.
Reduce heat to maintain a gentle simmer; cover and cook 5–7 minutes for set whites and jammy yolks, or 8–9 minutes for fully set yolks. Remove from heat. Zest the lemon over the dish, drizzle with remaining 1 tbsp olive oil, add lemon juice, and garnish with parsley and dill. Serve immediately.