Data concerning the combined effect of diet and exercise interventions on overall health in the elderly are scarce. The MED-E project's primary aim is to assess the effect of the different 3-month sustainable healthy diet (SHD) and multicomponent training (MT) interventions on several health outcomes in the elderly. A quasi-experimental study assigned older adults into four groups: (1) SHD, (2) MT, (3) SHD + MT, or (4) control group (CG). The SHD intervention included a weekly offer of a mixed food supply and individual and group nutritional sessions on the principles of an SHD. The MT groups were submitted to 50-min exercise sessions three times a week. The primary outcomes were blood biomarkers and metabolic profile alterations that were assessed pre- and post-intervention. Additionally, data on dietary intake and nutritional adequacy, physical fitness, body composition and anthropometry, cognitive function, quality of life, and geographical data were assessed at the same time points. The MED-E project's study protocol and future results will add to knowledge about the importance and beneficial contribution of combined SHD and MT interventions on healthy ageing policies.