The reactive chemistry of isoprene, which is the dominant hydrocarbon in biogenic emissions, has a controlling influence on the composition and cleansing capacity of the global atmosphere. Despite decades of research, isoprene continues to offer surprises in its atmospheric chemistry, particularly in environments with low-to-moderate levels of nitrogen oxides (NOx). Here, we probe the isoprene photochemical oxidation in this “intermediate-NOx” regime by examining the yield distributions of two major oxidation products, i.e., methacrolein and methyl vinyl ketone, using chamber experiments and aircraft measurements. Such a dataset provides strong constraints on the kinetics of the isoprene peroxy radical interconversion—a newly discovered mechanism that essentially governs the isoprene oxidation carbon flow. Insights from measurement-model comparisons further reveal an efficient operation of this mechanism across all the vegetated continents over the globe, constantly modulating the radical cycling and contributing to the formation of ozone and organic aerosols in the atmosphere.