Substance Use Disorders (SUD) lead to brain structural and functional deficits associated with cognitive and social functioning in affected individuals and can impact on treatment outcomes. The lack of behavioural autonomy is underpinned by direct reward, high impulsivity and difficulties in planning behaviour. The motor cortex — as part of a neural mechanism accounting for action and intention — plays a fundamental role in complex cognition, motor performance and coordination. The study sample consisted of 74 abstinent patients, aged 18–60 years, diagnosed with alcohol and/or cocaine dependence who were all inpatients at a private treatment programme for drug/alcohol dependence in South Africa. The main questions addressed were whether motor timing abilities would improve over time (as a function of recovery) in patients admitted to a rehabilitation programme for SUD, and if there were between-group differences. Timing abilities in SUD improved with prolonged abstinence. Timing in decision making (cognitive control) did not improve over time, nor did movement coordination. Rhythmic abilities and synchronisation with external events, as well as spatial abilities, improved with prolonged abstinence. The recovery of rhythmic and synchronisation abilities differed between the groups. This study shows for the first time that motor timing abilities can recover significantly with prolonged abstinence with differences in recovery between SUD populations. Improvements in interval timing only (both in time and in space) were observed. Not all motor timing abilities, and not every type of SUD, recovered equally, thereby suggesting that different substances may affect the brain differently with regard to timing abilities. These findings suggest that motor timing should further be investigated in different clinical settings.