This study evaluated the effect of housing systems (HS) and chicken genotypes (CG) on the behavior, morphometrics, and carcass traits of Naked Neck cockerels. In total, 405 males between 6 to 16 weeks old were studied. A randomized complete block design in factorial arrangement, with 9 treatments of 3 replicates with 15 birds each, was applied. Treatments consisted of 3 housing systems (Enriched indoor aviary system, Semi-intensive free-range system, and Intensive indoor system) and three chicken genotypes (full feathered (FF), partial feathered (PF), and Naked Neck (NN)). Behavior (walking, jumping, running, drinking, foraging & feeding, standing, sitting, aggressiveness, dust bathing, and wing flapping), morphometrics (body, keel, drumstick, and shank length, wing spread, drumstick and shank circumference), and carcass traits (pre-slaughter, shank, head, empty intestine, empty gizzard, liver, heart, neck, carcass, leg quarter, thigh, drumstick, and breast weight, and carcass yield) were evaluated. Scratching, perching, feeding, and dust bathing behaviors were more pronounced (p ≤ 0.05) in Semi-intensive free-range system reared birds whereas Naked Neck genotype exhibited higher (p ≤ 0.05) scratching, preening, jumping, and feeding behaviors. Birds reared under Enriched indoor aviary system revealed higher (p ≤ 0.05) keel and drumstick length while body, drumstick and shank length, and drumstick and shank circumference were greater (p ≤ 0.05) in full feathered genotype. Neck and carcass were heavier (p ≤ 0.05) in birds reared under Enriched indoor aviary system and Semi-intensive free-range system whereas pre-slaughter, carcass, and breast weight were better (p ≤ 0.05) in full feather genotype. In conclusion, the optimal housing system is genotype specific. The Semi-intensive free-range system is recommended for Naked Neck chickens to best express their natural scratching behavior, and for Partial Feathered chickens to promote dust bathing. The Enriched indoor aviary system is recommended for Full Feathered chickens to maximize carcass yield and muscling. Therefore, matching genotype to housing system is crucial for optimizing both welfare and production outcomes.