Abstract Satellite studies have shown that some of the deepest convection with high lightning flash rates occurs downstream of the Andes in subtropical South America (SSA). Using high resolution ground‐based observations in SSA, we explore the relationship between lightning and radar‐inferred storm microphysics. Results show these storms have significantly larger 35‐dBZ volumes and more graupel per lightning flash compared to storms in the U.S. We then test microphysics‐based lightning parameterizations for storms in SSA on a 1‐km convection‐permitting simulation of a mesoscale convective system. Results from the simulation match well with observed flash rates. If parameterizations based on U.S. storms had been applied, flash rates would have been overestimated by a factor of eight. These results suggest that storms in SSA are fundamentally different compared to storms in the U.S., and caution should be exercised when applying microphysics‐based lightning parameterizations in different regions of the world.