Land sharing strategies in agricultural landscapes need to allow for organisms to move between natural areas and different crops within an agro-ecological landscape in order to reduce extinction probability and the negative effects of small isolated populations. In this study, we tested whether legume or wheat fields differed in their effects on reptiles’ movement patterns. We conducted our study in an agro-ecosystem consisting of small isolated natural habitat patches nested within agricultural fields. We trapped reptiles in sampling arrays before and after harvest in both wheat and legume fields, and in adjacent natural habitat patches. For both crops, prior to harvest, we found an increase in movements of Trachylepis vittata, the most common reptile in our study, from the natural habitat patches into fields, but negligible movement in the opposite direction. In both crops before harvest, the individuals that moved into the fields were adults of better body condition than those remaining in the natural habitat patch, suggesting that long-distance movements were only possible for individuals with high prospective fitness. After harvest, no movements were documented between wheat fields and natural habitat patches. However, in legume fields, a high symmetrical movement (i.e. in both directions) of individuals of similar body condition between fields and natural habitat patches took place. Importantly, newborn lizards were only found in the natural habitat patches and in post-harvest legume fields. Our results suggest that agricultural heterogeneity, through a mixture of crop types may mitigate some of the negative effects of particular crops on biodiversity. As crop rotation between wheat and legume fields is common worldwide, our findings highlight the importance of creating an agricultural mosaic to enhance biodiversity permeability within the agricultural matrix.