IAA carboxyl methyltransferase 1 (IAMT1) converts auxin (IAA) into its methyl ester (MeIAA). IAMT1 is reportedly critical for shoot development of Arabidopsis, but its metabolic role has remained unclear. We previously discovered auxin methylation during root nodule symbiosis in Lotus japonicus, and are currently investigating its metabolic role in this context. The symbiotic organ, the nodule, requires spatiotemporal regulation to accommodate rhizobia during its formation. Nodule formation involves bacterial infection of the root epidermis, followed by primordium formation in the adjacent layers root cortex, steps that must be spatiotemporally coordinated. While IAMT1 expression was induced in epidermis during infection, its function was required in cortex, where it promoted nodule development. This suggests a spatiotemporal role of IAMT1 across tissue layers. Endogenous MeIAA increased in roots after epidermal infection. Exogenous MeIAA, in combination with cytokinin, a key phytohormone in nodule primordium formation, was sufficient to induce organogenesis in rhizobia-susceptible zone in the absence of rhizobia. Our results could provide evidence for the role of auxin methylation in the spatial regulation of the site of organogenesis.