Double-bond transposition in alkenes (isomerization) offers opportunities for the synthesis of bioactive molecules, but requires high selectivity to avoid mixtures of products. Generation of Z-alkenes, which are present in many natural products and pharmaceuticals, is particularly challenging because it is usually less thermodynamically favorable than generation of the E isomers. We report a β-dialdiminate-supported, high-spin cobalt(I) complex that can convert terminal alkenes, including previously recalcitrant allylbenzenes, to Z-2-alkenes with unprecedentedly high regioselectivity and stereoselectivity. Deuterium labeling studies indicate that the catalyst operates through a π-allyl mechanism, which is different from the alkyl mechanism that is followed by other Z-selective catalysts. Computations indicate that the triplet cobalt(I) alkene complex undergoes a spin state change from the resting-state triplet to a singlet in the lowest-energy C-H activation transition state, which leads to the Z product. This suggests that this change in spin state enables the catalyst to differentiate the stereodefining barriers in this system, and more generally that spin-state changes may offer a route toward novel stereocontrol methods for first-row transition metals.