The experience of shared flow refers to the optimal balance between challenge and ability for a given task, resulting from interpersonal action in a group situation. The performance of Javanese gamelan is an ideal setting to investigate shared flow, due to the requirement that all performers on varying instrumental parts work harmoniously, allowing for shared flow and its native equivalent, ngeli. To minimise the disruption of flow, while still measuring it continuously, one way to assess a person's state is by measuring physiological responses of the sympathetic (i.e., fight-or-flight) system, namely heart rate and skin conductance. Flow has been related to physiological signatures, and shared actions in music-making have been related to synchronised physiology. However, to our knowledge, no study yet has directly investigated the links between shared physiology and shared flow. Therefore, this study aimed to assess the associations between flow states, physiological synchrony, and Javanese gamelan playing. Subsequently, we tested for differences between advanced and beginner groups playing traditional gamelan pieces and improvising. Firstly, a factor analysis revealed a two-factor solution of Awareness and Absorption for self-reported shared flow. Next, using inter-subject correlation to assess synchrony and circular shuffling to infer significance, we found a greater proportion of significance in traditional playing compared to improvised playing for the experienced group, and the opposite for the beginner group. Lastly, linear mixed models revealed largely positive associations between synchronised physiology and shared flow during improvised playing, and negative associations during traditional playing, regardless of experience levels. This study demonstrates methodological possibilities for the quantitative study of shared flow in music-making contexts, and potential differences in shared flow experience in improvised and traditional, or prescribed, playing.