The continuously growing global population and intensifying climatic change pose increasing challenges to plants, especially crop species, in adapting to and surviving within their environments. Crop productivity and resilience are determined by key agronomics traits such as the flowering time, fruit or seed production, and responses to abiotic and biotic stresses. Among these, flowering time is particularly significant, as it integrates a wide range of environmental cues, starting from seasonal fluctuations to metal-induced stresses. Post-translational modifications (PTMs) of proteins governing these traits are tightly controlled and play crucial roles in modulating protein function. PTMs are thus emerging as crucial modulators in plant adaptive responses. In this chapter, we explore the significance of these traits in the production of sustainable crops, capable of withstanding environmental challenges. We highlight the importance of PTMs in manipulating or enhancing agriculturally important traits. Additionally, we discuss the current advances in modern techniques used to detect and characterise PTMs associated with particular traits as well as efforts to manipulate PTMs in various crops to enhance the yield and quality. We also address potential trade-off and unintended consequences of targeting PTMs. Finally, we emphasise about the relevance of proteomics as a powerful tool for advancing crop improvement strategies under environmental stress.