We investigated task-set control processes and chunking in 16 novices and 16 amateur musicians, who produced unimanual rhythms in three experimental conditions: low-level timing tasks required isochronous tapping at constant target durations; sequencing tasks consisted of individual rhythmic patterns comprising multiple target durations; the task-set control condition required alternations between two rhythmic patterns. According to our hierarchical timing control model conditions differed in their task-set control demands necessary to provide rhythm programs for the sequencing of individual intervals. Transitions at predicted chunk boundaries were marked by increased frequencies of sequence errors, relative lengthening of intervals preceding the switch to a new rhythm chunk, and increased variabilities in intervals immediately following a switch. Amateur musicians showed superior timing (less variability) in complex rhythm tasks. Moreover, they made fewer sequence errors than novices at set-switch points with their error patterns suggesting that they relied on larger chunks compared with novices. Our findings elucidate the time course of task reconfiguration processes in rhythm production and the role of chunking in the context of musical skill.