The global restriction on antibiotic growth promoters has intensified the search for phytogenic alternatives capable of supporting sustainable poultry production without compromising animal health and food safety. Despite increasing interest in botanical feed additives, information on their organ safety under different production environments remains limited. This study evaluated the effects of dietary inclusion of a Piper guineense leaf–seed blend on liver and kidney integrity in broiler chickens reared under deep litter and battery cage housing systems. A total of 288 one-day-old Cobb 500 broiler chicks were assigned to a 2 × 4 factorial arrangement consisting of two housing systems (deep litter and battery cage) and four dietary inclusion levels (0, 0.5, 1.0, and 1.5%) of a Piper guineense leaf–seed blend (2:1 ratio). Each treatment was replicated four times with nine birds per replicate. Following a six-week feeding trial, liver and kidney samples were collected for histopathological examination, while renal glomerular transvertical diameter was assessed using histomorphometry. Renal tissues remained normal up to 0.5% inclusion in both housing systems. However, tubular degeneration was observed at 1.0% and 1.5% inclusion levels in battery cage birds, whereas degeneration occurred only at 1.5% in deep litter birds, suggesting greater renal tolerance under deep litter management. Hepatic alterations increased with dietary inclusion level in battery cage birds, with severe hepatocellular degeneration, pyknosis, and necrosis observed at 1.5% inclusion. In contrast, birds reared under deep litter exhibited mild-to-moderate hepatic alterations across the supplemented groups. Glomerular diameter was lowest in battery cage birds fed 1.5% Piper guineense. These findings indicate that the organ safety threshold of dietary Piper guineense is influenced by housing system and that liver and kidney responses differ between production environments. Consideration of housing conditions may therefore be important when evaluating phytogenic alternatives for sustainable poultry production.