Phosphorus magnetic resonance (MR) spectroscopy was used to measure the recovery kinetics of calculated cytoplasmic metabolically active adenosine diphosphate (ADP) after exercise in normal subjects and patients with mitochondrial myopathies. These kinetics have previously been fitted with a single exponential function, despite a complex time-dependent undershoot in many subjects. By considering the transition from ischemic-exercise to perfused-recovery as a step function input, a second-order linear system was developed yielding a step response function to fit the ADP recovery. Using this method, an average improvement in fit of 23% resulted in a significant improvement in the characterization of ADP recovery for all normal subjects with substantial undershoot. The patient group had a comparable improvement in fit of 11%. Fitting the ADP recovery with a second-order step response function can provide significantly better characterization of muscle oxidative metabolism in vivo.