In this article, we develop a dynamic model to show how membership in agricultural cooperatives influences smallholder farmers' decisions to invest in organic soil amendments and chemical fertilizer. The model considers management decisions of heterogonous producers within an intertemporal framework, with the decision to join the cooperative assumed to be endogenous. Farm‐level data of apple farmers from three provinces in China are used to estimate the impact of cooperative membership on investment in organic soil amendments and chemical fertilizer. A recursive bivariate probit model that accounts for potential endogeneity of cooperative membership and selection bias is employed in the empirical analysis. The empirical results show that cooperative membership exerts a positive and statistically significant impact on the likelihood of investing in organic soil amendments. The findings also reveal that tenure security, human capital, farm size, and access to credit positively and significantly influence the probability of a farmer joining a cooperative and the likelihood of investing in soil quality measures.