Music engagement is an essential part in many people's everyday life. A large body of research has provided evidence for the beneficial effects of music engagement on health and well-being. Nevertheless, most of the findings are limited to music listening, music therapy, music as a profession or music education. In the present study, we examined the potential effects of the quality of motivation to engage in music making (autonomous vs. controlled) on flow and well-being. We tested the prediction by Self-Determination Theory that autonomous forms of motivation are related to higher well-being. Furthermore, we examined if flow experiences during music making might account for this association in an online daily diary study with 975 hobby musicians. Daily autonomous motivation to make music, flow (two subscales: fluency and absorption), and subjective well-being (life satisfaction, positive and negative affect) were assessed each day for ten consecutive days. Multilevel structural equation models indicated that there was a positive effect of autonomous motivation on life satisfaction and positive affect that was mediated by both subscales of flow, with fluency of performance at both the within- and between person level and absorption only at the within-person level. Further, there was a negative indirect effect on negative affect via fluency on the within-person level. This study provides evidence for the importance of autonomous motivation in hobby music making with regard to subjective well-being and highlights investigating the effects on a within-person level. Results further suggest the experience of flow as a potential mediating mechanism.