Reaction with ozone is an important atmospheric removal process for alkenes. The ozonolysis reaction produces carbonyls and carbonyl oxides (Criegee intermediates, CI), which can rapidly decompose to yield a range of closed shell and radical products, including OH radicals. Consequently, it is essential to accurately represent the complex chemistry of Criegee intermediates in atmospheric models in order to fully understand the impact of alkene ozonolysis on atmospheric composition. A mechanism construction protocol is presented which is suitable for use in automatic mechanism generation. The protocol defines the critical parameters for describing the chemistry following the initial reaction, namely the primary carbonyl/CI yields from the primary ozonide fragmentation, the amount of stabilisation of the excited CI, the unimolecular decomposition pathways, rates and products of the CI, and the bimolecular rates and products of atmospherically important reactions of the stabilised CI (SCI). This analysis implicitly predicts the yield of OH from the alkene–ozone reaction. A comprehensive database of experimental OH, SCI and carbonyl yields has been collated using reported values in the literature and used to assess the reliability of the protocol. The protocol provides estimates of OH, SCI and carbonyl yields with root mean square errors of 0.13 and 0.12 and 0.14, respectively. Areas where new experimental and theoretical data would improve the protocol and its assessment are identified and discussed.