Anthropogenic modifications to the landscape have altered several ecological processes worldwide, creating new ecological boundaries at the human/wildlife interface. Outbreaks of zoonotic pathogens often occur at these ecological boundaries, but the mechanisms behind new emergences remain drastically understudied. Here, we test for the influence of two types of ecosystem boundaries on spillover risk: (1) biotic transition zones such as species range edges and transitions between ecoregions and (2) land use transition zones where wild landscapes occur in close proximity to heavily impacted areas of high human population density. Using ebolavirus as a model system and an ensemble machine learning modeling framework, we investigated the role of likely reservoir (bats) and accidental host (primates) range edges and patterns of land use (defined using SEDAC categories) on past spillover events. Our results show that overlapping species range edges and heightened habitat diversity increase ebolavirus outbreaks risk. Moreover, we show that gradual transition zones, represent by high proportion of rangelands, acts as a buffer to reduces outbreak risks. With increasing landscape changes worldwide, we provide novel ecological and evolutionary insights into our understanding of zoonotic pathogen emergence and highlight the risk of aggressively developing ecological boundaries.