The focus of this research is on analysing the effects of institutional quality and trade agreements on Indonesia bilateral trade in four commodity groups in the era of global value chains (GVSs). Employing a panel data gravity model of Indonesian export of four commodities to Indonesia’s 18 trading partners from 2000 to 2018, and estimating the Feasible Generalized Least Squares (FGLS) and the Poisson Pseudo Maximum Likelihood Method (PPML), the results of this study find that institutional quality plays a different role in explaining Indonesia’s export performance of those four commodities, despite the fact that institutions contribute positively. Regarding raw material and capital goods export, trading partner institutions are significant factors for Indonesian export of the two commodities. On two commodities that are relevant to Indonesia participation in the global value chain, exported intermediates and consumer goods, we find that although both domestic institutions and trading partner institutions are significant to Indonesian export, but we argue that domestic institutions contribute more. This study also reveals that through tariff reductions, Indonesian trade agreements are significant regarding export of intermediate and consumer goods, but less so for raw material and capital goods.