Aim To examine the effects of a multifactorial intervention on frailty and functional health among community‐dwelling older adults, a 6‐month randomized, controlled, cross‐over trial was carried out within the Hatoyama Cohort Study. Methods A total of 77 pre‐frail or frail older adults (mean age 74.6 years) were randomly allocated to an immediate intervention group (IIG; n = 38) or delayed intervention group (DIG; n = 39). The IIG participated in a twice‐weekly multifactorial intervention comprising resistance exercise, nutritional education and psychosocial programs. No intervention was given to the DIG during the initial 3‐month period, and both groups were crossed over for the latter 3‐month period. Pre‐frailty and frailty were determined by using the Check‐List 15, which was validated against Fried's frailty criteria. Effects of the intervention on primary (Check‐List 15 score and frailty status) and secondary outcomes (physical and psychosocial functions, and nutritional intake) were examined for both 3‐month periods. Results As compared with the DIG, the IIG had significant reductions in Check‐List 15 score (−0.36 points; 95% CI −0.74 to −0.03), frailty prevalence (−23.5%, 95% CI −40.4 to −6.7), Timed Up and Go test (−0.25 s, 95% CI −0.47 to −0.08), and Geriatric Depression Score (−0.92 points, 95% CI −1.44 to −0.39), and improvements in the Dietary Variety Score (0.65 points, 95% CI 0.05–1.25), and protein (1.9% E, 95% CI 1.1–2.7) and micronutrient intakes at 3 months, all of which, excluding protein and micronutrient intakes, persisted at 6 months. The DIG showed similar intervention effects in the latter 3‐month period. Conclusions This 3‐month multifactorial intervention reduced frailty and improved functional health. These intervention effects persisted for at least 3 months post‐intervention. Geriatr Gerontol Int 2017; ••: ••–••.