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The purpose of this study was to analyze the mediating and combined effects of trust and satisfaction in a collaborative activity, while considering the effects of the performance of innovation in an Industry–Public Research Institute (I–PRI) collaboration. Data used in this study was collected through a survey targeting Small and Medium-Sized Enterprises (SMEs) in the INNOPOLIS Daedeok innovation cluster in Korea. PLS-SEM and fsQCA were used for the analysis of data collected. The results of this study show that trust mediates the relationship between collaboration and satisfaction, while satisfaction mediates the relationship between collaboration, and the performance of innovation, as well as the relationship between trust and the performance of innovation. In addition, it was confirmed that collaboration, trust, and satisfaction jointly affect the performance of innovation in I–PRI collaborations. Additionally, it was discovered that in-order to increase the performance of innovation - required to secure and maintain a competitive advantage; through I–PRI collaborations—SMEs need active collaboration with PRIs, and advanced management skills; to build mutual trust, and improve satisfaction. Finally, the theoretical implications of the factors that affect the performance of innovation in I–PRI collaborations were presented.