5-methylcytosine (m⁵C) is a common RNA modification with important regulatory roles in gene expression. In Arabidopsis thaliana, enzymes like TRM4B/NSUN2 catalyse cytosine methylation, while other candidate methyltransferases, DNMT2, TRM4A, and RCMT9, are less well characterized. The role of RCMT9 in RNA methylation remains largely unexplored. Using bisulfite RNA sequencing, we observed an approximately 50% reduction in global m⁵C levels in rcmt9 mutant seedlings compared to wild type. Interestingly, rcmt9 plants exhibited increased leaf size under blue light, suggesting a role for RCMT9 in light-dependent developmental regulation. To investigate subcellular localization and expression, we generated RCMT9-AtCer and AtCer-RCMT9 translational fusions and transiently expressed them in Nicotiana benthamiana leaves. These constructs showed reduced fluorescence under confocal microscopy, despite elevated steady-state mRNA levels. Fluorescence was restored upon treatment with the proteasome inhibitor Bortezomib, supporting a model in which RCMT9 is regulated via proteasomal degradation, specifically Ubiquitination. In summary, our results establish RCMT9 as a key player in RNA m⁵C methylation in Arabidopsis and suggest that its abundance might be post-translationally regulated.