How music training and expertise influence non-musical abilities is a widely researched topic. Most studies focus on the differences between adult professional musicians and non-musicians, or examine the effects of intensive instrumental training in childhood. However, the impact of music programs developed in regular school contexts for children from low-income communities is poorly explored. We conducted a longitudinal training study in such communities to examine if collective (Orff-based) music training enhances fine motor abilities, when compared to a homologous training program in sports (basketball), and to no specific training. The training programs in music and sports had the same duration, 24 weeks, and were homologous in structure. A pre-test, training, post-test and follow-up design was adopted. Children attending the 3rd grade (n = 74, 40 girls; mean age 8.31 years) were pseudorandomly divided into three groups, music, sports and control that were matched on demographic and intellectual characteristics. Fine motor abilities were assessed with the Purdue pegboard test (eye-hand coordination and motor speed, both subsumed under manual dexterity, and bimanual coordination) and with the Grooved pegboard (manipulative dexterity) test. All groups improved in manipulative dexterity that was not affected by type of training. On bimanual coordination and manual dexterity, however, a robust and stable advantage of music training emerged. At the end of training (post-test), children from the music group significantly outperformed children from the sports and control groups, an advantage that persisted at follow-up 4 months after training at the start of the following school year. Also, at follow-up none of the children from the music group were performing below the 20th percentile in the Purdue pegboard subtests and more than half were performing at the high end level (>80th percentile). Children from the sports group also improved significantly from pre- to post-test but their performance was not significantly different from that of the control group. These results show that an affordable, collective-based music practice impacts positively on fine-motor abilities, a finding that is relevant for a better understanding of the impact of music in childhood development, and that may have implications for education at the primary grade.