Current bioenergy production systems—aimed at replacing fossil fuels in the transport sector—have been linked to a wide range of environmental impacts, including biodiversity losses. This is mainly because they derive from food crops (i.e., maize, sugarcane, oil palm, soybeans, and rapeseed, among others), leading to direct and indirect land-use changes in areas of high biodiversity value. However, the potential impacts of novel, non-food based bioenergy production systems on biodiversity remains unclear. Microalgal production systems, which make use of microscopic prokaryotic and eukaryotic photosynthetic organisms, have the potential to become a future source of biofuels for the transport sector, though little is known about the potential conflicts of large-scale microalgal cultivation and biodiversity losses. Here, we use a GIS-based Multiple-Criteria Decision Analysis (MCDA) to select the most suitable areas for large-scale microalgal cultivation. We then explore a scenario in which 30% of transportation demand is met from algal biofuels, showing countries where minimal or maximal conflicts between microalgal cultivation and presence of areas of high ecological importance are expected to occur. Our results illustrate the countries in which algal biofuel production can be scaled up while avoiding significant impacts to biodiversity.