Chilli pepper (Capsicum annuum L.) is susceptible to Pectobacterium carotovorum subsp. carotovorum (Pcc), the causal agent of soft rot disease in crops. Understanding the molecular principles of systemic acquired resistance, which is poorly understood in chilli pepper, represents an important step towards understanding inducible defence responses and can assist in designing appropriate intervention strategies for crop disease management. Accordingly, we investigated (via real-time PCR and metabolomics profiling) the molecular response of chilli pepper to Pcc by characterisation of the crucial metabolic regulators involved in the establishment of defence response. We profiled 13 key inducible defence response genes, which included MYB transcriptor factor, ethylene response element-binding protein, suppressor of the G2 allele of Skp1, cytochrome P450, small Sar1 (GTPase), hydroxycinnamoyl-CoA:quinate hydroxycinnamoyl transferase, pathogenesis-related protein 1a, endo-1,3-β-glucanase, chitinase, proteinase inhibitor, defensin, coiled-coil-nucleotide-binding site-leucine-rich repeat (CC-NBS-LRR) resistance and phenylalanine ammonia lyase. In addition, we determined metabolomic shifts induced by Pcc in pepper. The PCR results revealed a significant induction of the selected plant defence-related genes in response to Pcc inoculation; the metabolomic profiling showed that of 99 primary metabolites profiled the quantities of acetylcarnitine, adenosine, adenosine 3',5' cyclic monophosphate, guanosine 3',5' cyclic monophosphate and inosine decreased in pepper leaves inoculated with Pcc.