Steady increases in human population size and resource consumption levels are driving rampant agricultural expansion and intensification in some of the world's most pristine ecosystems. Habitat loss caused by agriculture puts the integrity of ecosystems at risk, and as a consequence, threatens the persistence of human societies that rely on ecosystem services to produce resources. Here we develop a spatially explicit model describing the coupled dynamics of an agricultural landscape and human population size to study the effect of different land-use management strategies, defined by the levels of agricultural clustering and intensification, on the sustainability of the social-ecological system. We show how gradual agricultural expansion can cause natural habitat to undergo a percolation transition leading to abrupt habitat fragmentation that feedbacks on human's decision making, causing faster agricultural expansion and aggravating habitat loss and fragmentation. We found that agricultural intensification to spare land from conversion is a successful strategy only in highly natural landscapes and that clustering agricultural land is the most effective measure to preserve landscape connectivity and avoid severe fragmentation. Our work highlights the importance of preserving large connected natural fragments in agricultural landscapes to enhance sustainability.