Plant peptide hormones orchestrate growth, development and immunity by engaging membrane-resident receptor kinases. GmSubPEP, a defence-eliciting peptide derived from a subtilase precursor, was initially isolated from soybean leaf extracts. Here we uncover an unexpected expansion of GmSubPEP variants with highly diverse sequences, yet each capable of triggering robust, tissue-specific pathogen resistance. Integrated transcriptomic and phosphoproteomic profiling shows that individual GmSubPEPs differentially activate overlapping and unique immune pathways, enabling fine-tuned defence modulation. Strikingly, genes generating these peptides and their receptors, termed GmSubPEP Receptors (GSPRs), are physically interspersed within a genomic cluster, and GSPRs exhibit differential binding affinities for their cognate peptide ligands. By unveiling how conserved subtilase precursor scaffolds diversify into specialized ligand–receptor pairs across legume lineages, our work reveals the role of SubPEP–GSPR modules in plant–microbe interactions and provides a framework for mining and engineering peptide–receptor modules to strengthen crop immunity.