Metabolism in plants and their secondary products play vital role in various signaling pathways governing ecological interactions including defense. Plant secondary metabolites are progressively used as food additives or bio-preservative agents and used for aromatic and culinary purposes. At molecular level, the MYB, bHLH, AP2/ERF, SPL, and NAC are some crucial transcription factors that regulate gene expression against biotic or abiotic stressors. The mevalonate pathway deals with HMG-CoA reductase, mevalonate-5-kinase, mevalonate-5-phosphate decarboxylase, and phosphomevalonate kinase, whereas DHAP synthase, chorismite synthase, DHQ dehydratase, and shikimate kinase are some of the most important enzymes of the shikimate pathway. Proteomics help to perceive a clear picture of the regulation of plant genome expression in response to different biotic and abiotic stressors that eventually couple with secondary metabolite production, and the same can also be used as complementary tools for functional analysis and biomarker discovery research. Plant secondary metabolites are essential for microbial interactions, quorum sensing, and plant defense. Genes such as CHS (chalcone synthase) and F3H (flavonoid 3-hydroxylase) regulate flavonoids, which influence nodulation and mycorrhizal symbiosis. Microbes such as Rhizobium, Pseudomonas, and arbuscular mycorrhizal fungi (AMF) influence these pathways, improving nutrient acquisition and resistance to diseases. These plant-microbe interactions highlight the possibility of sustainable agricultural and biotechnological uses. Alteration in the expression of differential proteins, variation in cellular protein localization and their accumulation patterns, and posttranscriptional and posttranslational modifications are often found associated with the presence of stressors. This chapter focuses on the understanding of protein profiling coupled with secondary metabolomics to study the cellular pathways associated with stress responses.