In a large mixing bowl, combine olive oil, fresh lemon juice, lemon zest, minced garlic, rosemary, oregano, thyme, parsley, salt, black pepper, smoked paprika, and red pepper flakes. Stir together with a fork or small whisk until well combined.
Pat chicken dry with paper towels, then cut into uniform 1.5-inch cubes. Add to the marinade, toss to coat thoroughly, cover, and refrigerate for at least 30 minutes and up to 4 hours (do not exceed 8 hours).
Cut the red onion and bell peppers into 1-inch chunks. Remove chicken from the fridge and let sit at room temperature for 10 minutes, then thread skewers alternating chicken, onion, and pepper pieces, leaving a small gap between each piece.
Preheat your grill to medium-high heat (400°F–450°F / 200°C–230°C) for 10–15 minutes, then oil the grates using a paper towel dipped in oil held with tongs.
Place skewers on the grill, close the lid, and cook 3 minutes per side undisturbed, rotating a quarter turn each time for a total of 10–12 minutes, until an instant-read thermometer reads 165°F (74°C).
Transfer skewers to a clean plate and rest for 3–5 minutes, then garnish with fresh chopped parsley and a squeeze of fresh lemon. Serve immediately.