Physical exercise, when practiced regularly and in adequate doses, is a proven nonpharmacological measure that helps to prevent and reverse noncommunicable diseases, as well as reduce mortality rates from any cause. In general, older adults perform insufficient physical activity and do not meet the doses recommended by the World Health Organization for the improvement of health through physical activity. However, there is little evidence on adequate doses of exercise in older people, especially in those with multimorbidity. Our main aim was to evaluate the effect of a 6-week intervention on health-related outcomes (body composition, hemodynamic and functionality changes) in 24 individuals aged 65 and older with multimorbidity in a randomized controlled trial. The intervention consisted of a very low volume (60 min per week) of low-to-moderate intensity exercise training (perception of effort from 3 to 6 on an 11-point scale). After the intervention, blood pressure was significantly (p = 0.038) reduced in the exercise group (EG), with a higher reduction in men. Furthermore, the EG decreased their waist circumference (p = 0.005), a proxy of abdominal adiposity, and demonstrated an increased likelihood (73%) that a randomly selected change in muscle mass score from the EG would be greater than a randomly selected change score from the control group. The exercise intervention was particularly effective in enhancing the functionality of older adults with multimorbidity, especially in walking speed and balance skills. Perceptually regulated intensity during exercise training seemed to be a very interesting strategy to train individuals with low physical fitness and comorbidities. This study is registered with Clinicaltrials.gov (NCT04842396).