Summary Complex side reactions drive capacity fade in modern Li-ion batteries and are a key factor in achieving extended battery lifetimes. Unfortunately, the interconnected nature of the reaction pathways means that optimizing one aspect of performance can result in a shift between benign and detrimental side reactions, and that simple Coulombic efficiency is unable to capture these differences. Because batteries are ultimately chemical reactors, reaction engineering principles can provide a suitable framework for understanding. The electrocatalytic systems of Li-O2 batteries and electrochemical CO2 reduction demonstrate both the importance of quantifying reaction selectivity and the key role that reactor geometry plays in this process. Recent findings from these fields suggest that battery side reactions should also be studied in reactors that have been optimized for analytics. In this reaction engineering context, we discuss the advantages and disadvantages of existing analytical tools and present pathways for designing new reactors that can directly evaluate Li-ion battery reaction selectivity. Quantification of selectivity and reaction parameters can direct materials design and improve lifetime prediction.