Modified nucleotides on RNAs have been investigated for over six decades for their potential role in regulating gene expression and protein synthesis across a wide range of organisms, from animals to plants and fungi, as well as in viral genetic materials. Among them, mRNA methylation stands out with its dynamic nature, which underscores the adaptability of the epitranscriptome in developmental transitions and response to environmental stress, especially in plants. Advances in next-generation sequencing methods have revealed the specific sequence contexts of mRNA methylation, uncovering their involvement in gene regulatory networks. Additionally, genetic perturbations on the writers, erasers, and readers of m6A and m5C expanded our understanding of the physiological function and the mode of action of these modifications. In this review, we highlight recent advances in understanding how mRNA fate decisions, mainly determined by m6A and m5C RNA methylation, shape stress response and development in plants.