Co-management, a governance system in which governmental authorities and local communities share resource management responsibilities, is increasingly recognized worldwide for its potential to reconcile natural resource conservation with livelihood goals. This case study examines the perceptions of diverse stakeholders regarding the effects of introducing both voluntary and government-led Individual Quota (IQ) systems in Japanese fishery co-management, spanning governance, economics, sustainability, and social aspects. Employing an integrated mixed method approach, the study combines qualitative interviews and questionnaires with quantitative analysis of before-and-after catch data. After the introduction of the voluntary IQ system in 2017, 67 % of the stakeholders acknowledged improvements in overall performance. The favorable findings from various perspectives reflect not only the stakeholders' profound confidence in the system but also their satisfaction with the matured co-management process. However, qualitative results from the case also indicate that the government-led IQ system implemented since 2022 primarily imposes rigidity on the existing voluntary system, while failing to provide sufficient incentives for fishers to transition effectively. Effective incentives are essential, including increased transparency in resource management, greater flexibility in managing catch quotas, and facilitating consensus on the liberalization of fishing vessel sizes. Continuous evaluation is crucial, and the government-led IQ system should be adaptively improved.