DNA methylation can be associated with phenotypic plasticity, yet how temperature shapes DNA methylation diversity in natural populations is unclear. Analyzing whole-genome bisulfite sequencing from 1075 Arabidopsis thaliana accessions grown at 10°C, 16°C, and 22°C, we quantified single-cytosine diversity using Jensen-Shannon Divergence (JSD). Diversity consistently peaked at intermediate methylation levels across the CpG, CHG, and CHH sequence contexts. Temperature modulated this diversity, primarily impacting intermediately methylated sites, with non-CG contexts (CHG and CHH) exhibiting increased diversity at warmer temperatures. Notably, at 22°C, CHH diversity patterns indicated altered balance between the RdDM and CMT2 pathways that regulate specific transposable element (TE) superfamilies. Furthermore, accessions from Southern Europe displayed higher non-CG diversity at 22°C compared to Northern European accessions. Our findings reveal that temperature influences the epigenomic diversity landscape, highlighting context-dependent plasticity, a dynamic interplay between silencing pathways, and potential geographic adaptation in response to environmental cues.