The purpose of the present study was to determine the effects of a proprioceptive training program on older adults, as well as to analyze the association between flexibility, balance and lumbar strength (physical fitness test) with balance ability and fall risk (functional balance tests). This study was a controlled, longitudinal trial with a 12-week follow-up period. Subjects from a population of older adults were allocated to the intervention group (n = 28) or to the usual care (control) group (n = 26). Subjects performed proprioceptive training twice weekly (6 specific exercises with Swiss ball and BOSU). Each session included 50 minutes (10 minutes of warm-up with slow walk, 10 minutes of mobility and stretching exercises, 30 minutes of proprioceptive exercises). The outcome variables were physical fitness (lower-body flexibility, hip-joint mobility, dynamic balance, static balance, and lumbar strength) and functional balance (Berg scale and Tinetti test). The experimental group obtained significantly higher values than the control group in lower-body flexibility, dynamic balance, and lumbar strength (p = 0.019, p < 0.001, and p = 0.034 respectively). Hip-joint mobility, dynamic balance, and lumbar strength were positively associated with balance ability (p < 0.001, p < 0.001, and p = 0.014, respectively) and the prevention of falls (p = 0.001, p < 0.001, and p = 0.017 respectively). These findings suggest that a 12-week proprioception program intervention (twice a week) significantly improves flexibility, balance, and lumbar strength in older adults. Hip-joint mobility, dynamic balance and lumbar strength are positively associated to balance ability and the risk of falls in older adults. This proprioceptive training does not show a significant improvement in hip-joint mobility or static balance.