Bamboo compost is a renewable organic material that can replace peat and enhance plant resistance to insect pests. However, its combined effects on tomato (Solanum lycopersicumL.) growth, defense responses, and underlying molecular mechanisms remain unclear. In this study, bamboo compost was incorporated into growing substrates at varying proportions (5–30%) to assess its impact on tomato seedling growth, physiological and biochemical traits, and the survival of the South American tomato leafminer, Tuta absoluta. Metabolomic and transcriptomic analyses were further integrated to characterize molecular changes associated with enhanced resistance. The results showed that 10% bamboo compost increased plant height and stem diameter by 25.91% and 10.19%, respectively, while higher proportions inhibited seedling growth. All bamboo compost treatments significantly reduced Tuta absoluta. larval survival, with the lowest day-10 survival (16%) observed under BC−20%. Multi-omics analyses identified 1553 and 2591 DEGs and 292 and 591 DAMs in the BC−10% vs. CK and BC−20% vs. CK comparisons, respectively; 290 differentially expressed transcription factor-encoding genes were identified across both comparisons. BC−20% showed broader defense-related transcriptional and metabolic reprogramming, including MAPK and phytohormone signaling, phenylpropanoid and flavonoid biosynthesis, and cutin and wax formation, but with reduced growth. Overall, BC−10% represents a suitable practical addition rate for promoting tomato seedling growth in peat-reduced cultivation substrates.