Body of Abstract: Chromatin profiling techniques have improved our understanding of chromatin structure and its role in transcriptional regulation. However, in all these methods, purifying nuclear DNA from organellar DNA remains challenging in plant genomes. For the Tn5 transposase-based epigenomic profiling methods, such as ATAC-seq, and CUT&Tag, purifying nuclei is even more critical since hyperactive Tn5 transposase also targets mitochondrial and chloroplast genomes. Contamination of nuclear DNA with organellar genomes may cause a significant proportion of sequencing reads to be discarded. Therefore, we developed a protocol for isolating high-quality nuclei free of interfering mitochondrial or plastid DNA from monocot and dicot species. In this protocol, nuclei were bound to Concanavalin A-Coated Magnetic Beads (Con-A Beads) and washed multiple times to minimize organellar DNA contamination. Concanavalin A, a carbohydrate-binding protein, can bind to different glycan structures of the extracellular matrix and immobilize cells and nuclei. We conducted ATAC-seq on nuclei that were purified with ConA. As expected, the ATAC-seq reads obtained from the ConA-purified nuclei had a significantly greater proportion of reads mapped to the nuclear genome than those not purified with ConA beads. We also performed H3K27me3 CUT&Tag on ConA purified nuclei, and there is a high similarity between H3K27me3 ChIP-seq and CUT&Tag data. The method of isolating nuclei using ConA beads described here yielded high-quality nuclei and improved the efficiency of ATAC-seq and CUT&Tag in plant genomes.