Proponents of short food supply chains (SFSC) have put their environmental benefits forward. Although most of the studies have focused on their climate change impact, the use of pesticides by farmers in SFSC has received little research attention. In this study, we investigate the effect of different types of SFSC on the application of pesticides in fruits and vegetables production. This study relies on data obtained from the 2010 agricultural census and two national surveys on the phytosanitary practices of fruits trees producers and market gardeners. This paper employs a multinomial endogenous treatments effect model in order to account for selection bias and endogeneity stemming both from observed and unobserved heterogeneity. The results demonstrate a lower use of pesticides for farmers selling through direct-to-consumer (DTC) channels and marketing channels with one intermediate (IMC) than those in longer food supply chains. In addition, the reduction effect of using DTC channels is twice that of IMC. We also show that the reduction of pesticides use is more important in market gardening than in arboriculture.