Farming systems in marginal or less favored areas of Europe have faced a multitude of challenges as a response to so-called “mega-trends”. A typical response has been land abandonment. The focus of this paper is on the farming systems of the Greek islands of Lesvos and Lemnos. These neighboring islands are geographically very similar but differ greatly in their farming systems, resulting in different responses to the same megatrends. While land abandonment is widespread in the small-scale olive groves of Lesvos, on Lemnos specialization towards animal and dairy products is more common. We performed land cover analysis and interviews with farmers in both areas, in two complementing rounds: one more quantitative that recorded recent changes and farmer rationales and a more qualitative one that investigated longer term trends and decision-making patterns. The analysis revealed that, among others, land ownership and inheritance patterns matter in both areas in different ways, leading to diverse trajectories. On Lemnos, as part of the traditional mixed-farming system (Mandra), land leasing is dominant, separating land users and landowners. Interviews also reveal the different symbolic capital, as olive trees on Lesvos are considered a family asset and not just a land use, something that cannot be said of the leased grazing lands on Lemnos. The market value of the different products is important, but the different trajectories also demonstrate how the rationales behind the responses to mega-trends can guide which trajectories will be dominant in the area. This article highlights the complexity and mix of local drivers and global trends that drive abandonment at both farm and the landscape scales and guides the formulation and application of agricultural policies and public resources for improved management of marginal areas.