Global biodiversity is rapidly declining and goals to halt biodiversity loss, such as the Aichi Biodiversity Targets, have not been achieved. To avoid further biodiversity loss and aid recovery some have argued for the protection of 50% or 30% of the Earth’s terrestrial land surface. We use a state of the art global land use model, LandSyMM, to assess global and regional human health and food security outcomes when potential area based strategies for conserving biodiversity are modelled. We find diet and weight changes in strictly enforced 30% and 50% land protection scenarios, cause an additional 5.1 million deaths in 2060. At a regional level, South Asia and Sub-Saharan Africa experience high levels of underweight-related mortality, causing an additional 200,000 deaths in these regions alone. Developed regions in contrast are less affected by protection measures. Our results highlight that radical measures to protect areas of biodiversity value may jeopardise food security and human health in the most vulnerable regions of the world.