The root-knot nematode (Meloidogyne incognita) poses a major threat to global agriculture by impairing root function, reducing nutrient uptake, and ultimately limiting seed development and crop productivity. This study investigated the molecular and metabolic defense responses of Cucumis metuliferus (prickly pear) to M. incognita infection. Gene expression and metabolic pathway reprogramming in M. incognita-infected roots were examined using integrated transcriptomics and metabolomics approaches. The identified genes were involved in stress responses and defense activation. Furthermore, metabolite profiling revealed significant shifts in secondary metabolite production, with an upregulation of defense-related compounds like jasmonic acid, salicylic acid, and prostaglandins. KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis highlighted critical pathways such as biotin metabolism and nucleotide metabolism, underscoring the adaptive metabolic responses of C. metuliferus plants. GO (Gene Ontology) analysis from the integrated transcriptomics and metabolomics data highlighted significant upregulation of enzymatic pathways, transporter activities, and reorganization of cellular structures. Furthermore, KEGG pathway analysis revealed activation of secondary metabolite biosynthesis, immune-related signaling pathways, and metabolic reprogramming including increased carbon metabolism and nucleotide biosynthesis. This study provides a valuable molecular framework for breeding of M. incognita-resistant cultivars, ultimately supporting more stable seed distribution and agricultural productivity in M. incognita-prone regions.