The study was carried out to compare the growth performance, gut microbiota, incidence of footpad dermatitis (FPD), leg weakness, physiological, and immunological responses in broilers kept in cage (CS) and floor pen (FS) rearing systems under a tropical environment. One-day-old male Cobb 500 chicks were allocated to either three-tiered wire-floored battery cages or floor pens with wood shavings. The body weight on day 42 and feed intake from days 1 to 42 of caged chickens were lower than those of chickens reared in floor pens. However, the caged chickens had significantly better overall (days 1–42) feed conversion ratios than those on floor pens. The FS system was detrimental to the incidence of FPD. The FS birds showed higher and lower caecal counts of Escherichia coli and Salmonellae, respectively than the CS birds. The FS birds had longer durations of latency-to-lie than their caged counterparts, which suggested that the former had a lower incidence of leg weakness. Higher serum basal concentrations of corticosterone, ovotransferrin and ceruloplasmin were noted in the FS chickens compared to the CS group. Antibody titre against Newcastle disease vaccinations was not affected by the rearing system. In conclusion, the cage rearing system appeared to benefit performance, the incidence of FPD, physiological response, fear reactions, and intestinal population of E. coli in broiler chickens under the hot and humid tropical conditions. However, raising broilers on floor pens improves body weight and leg strength, and reduces the caecal Salmonellae population compared to caged broilers. HIGHLIGHTS Caged broilers have better feed efficiency and lower caecal Escherichia coli population and incidence of food-pad dermatitis than those on floor pens. Raising broilers on floor pens improves body weight and leg strength, and reduces the caecal Salmonellae population compared to caged broilers. Broilers on floor pens are more physiologically distressed than their caged counterparts.