Bone morphogenetic proteins (BMPs) play diverse roles in mouse embryonic stem cell (mESC) biology. Recent studies suggest that BMPs induce multiple cell fates and enhance mESC heterogeneity by cross-activating multiple signaling pathways. Although BMPs primarily signal through SMAD1 and SMAD5 in mESCs, their roles remain incompletely defined. Here, we investigated the SMAD signaling pathway using Smad1/5 double knockout (S1/5 dKO) mESCs. While SMAD1/5 depletion may influence mESC heterogeneity, single-cell RNA sequencing (scRNA-seq) revealed only minor differences between S1/5 dKO and WT cells, suggesting that the observed changes are not because of altered cell states. Chromatin immunoprecipitation sequencing (ChIP-seq) demonstrated that SMAD1/5 recruit the histone demethylase KDM1A/LSD1 to specific genomic regions, where it removes H3K4me1/2 marks associated with enhancers. Published scRNA-seq data from Kdm1a-deficient mESCs during embryoid body differentiation further supported this mechanism. This study reveals a transcriptional repression mechanism of SMAD1/5, involving KDM1A-dependent H3K4me1/2 depletion and the regulation of cell type-specific gene expression programs.