As participation in wheelchair sports increases, the need of quantitative assessment of biomechanical performance indicators and of sports- and population-specific training protocols has become central. The present study focuses on junior wheelchair basketball and aims at (i) proposing a method to identify biomechanical performance indicators of wheelchair propulsion using an instrumented in-field test and (ii) developing a training program specific for the considered population and assessing its efficacy using the proposed method. Twelve athletes (10 M, 2 F, age = 17.1 ± 2.7 years, years of practice = 4.5 ± 1.8) equipped with wheelchair- and wrist-mounted inertial sensors performed a 20-metre sprint test. Biomechanical parameters related to propulsion timing, progression force, and coordination were estimated from the measured accelerations and used in a regression model where the time to complete the test was set as dependent variable. Force- and coordination-related parameters accounted for 80% of the dependent variable variance. Based on these results, a training program was designed and administered for three months to six of the athletes (the others acting as control group). The biomechanical indicators proved to be effective in providing additional information about the wheelchair propulsion technique with respect to the final test outcome and demonstrated the efficacy of the developed program.