Aging is associated with the impairment of health and functional capacity, and physical exercise seems to be an effective tool in frailty prevention and treatment. The purpose of this study was to present the methodology used in the EXERNET-Elder 3.0 project that aims to evaluate the immediate and residual effects and of a multicomponent exercise training program called Elder-fit on frailty, fitness, body composition and quality of life, and also to analyse a possible dietary intake interaction according to health and metabolic status. A total of 110 frail and pre-frail elders participated in this study and were divided into a control group (CG = 52) and an intervention group (IG = 58). The IG performed a supervised multicomponent exercise training program of 6 months and 3 days per week, which included strength, endurance, balance, coordination and flexibility exercises, while the CG continued with their usual daily activities. Both groups received four speeches about healthy habits along the project. Four evaluations were performed: at baseline, after 3 months of training, at the end of the training program (6 months) and 4 months after the program had ended to examine the effects of detraining. Evaluating the efficacy, safety and feasibility of this program will help to develop efficacious physical interventions against frailty. Further, protocols should be described accurately to allow exercise programs to be successfully replicated.