The objective of our paper is to provide an explanation for the lack of joint adoption by farmers of cleaner technologies in banana production, specifically fallow period (FP) and disease-free seedlings (DFS). Our hypothesis is that while these technologies are synergistic from an agronomic and environmental perspective, and thus efficient from a social interest perspective, they are substitutable rather than complementary from a farmer’s private interest perspective. In other words, farmers receive lower returns from adopting both technologies together than from adopting them in isolation. To test this hypothesis, we present a unified empirical framework for assessing complementarity. We estimate a structural model of complementarity that overcomes the unobservable heterogeneity bias found in previous models using a database of 607 banana farmers in the French West Indies. Our results support our hypothesis, showing a substitution effect between FP and DFS rather than a complementarity effect. Moreover, we observe a contrasting profile of adopting farmers: smallholders who are reluctant to change adopt FP, while more specialized farmers who anticipate a pesticide ban adopt DFS. A public policy that promotes joint adoption should compensate smallholders for the cost of the DFS technology, while compensating more productive farmers for leaving their land fallow.