MethMotif (https://methmotif.org) is a publicly available database that provides a comprehensive repository of transcription factor (TF)-binding profiles enriched with DNA methylation patterns. Since its inception in 2019, the platform has evolved to incorporate expanded datasets and advanced functionalities, deepening our understanding of context-specific TF functions. In its 2024 release, MethMotif expands its initial collection from 509 to over 700 position weight matrices (PWMs), all annotated with DNA methylation profiles. A key advancement of this update is the segregation of TF-binding motifs based on cofactors and DNA methylation status, allowing researchers to explore how gene ontology (GO) annotations and TF target genes can differ under varying cofactor contexts. MethMotif now supports two additional species: Mus musculus and Arabidopsis thaliana, broadening its applicability for comparative and translational research. By incorporating cofactor-based binding motifs, methylation profiles, and precomputed GO enrichments, MethMotif stands out as the first and only TF-binding motif database to integrate context-specific PWMs with epigenetic information, thus enabling deeper insights into the regulatory mechanisms governing gene expression.