ChIP-seq is a commonly used method to characterize chromatin-associated features on a genome-wide basis. A common set of steps for a ChIP-seq procedure prior to sequencing includes crosslinking, nuclei extraction, chromatin shearing, immunoprecipitation, elution, reversal of crosslinks, and library preparation. Plant material can be challenging to process for ChIP-seq analysis due to the unique attributes of plant cells that impair success. Here, we describe an effective ChIP-seq sample preparation method that is optimized for generating robust libraries from complex plant materials. In particular, we identify time as a critical parameter for effective coupling of ChIP-seq sample preparation with a commercially available kit to generate robust NGS libraries in-house. The resulting protocol is a cost-effective strategy to generate reliable ChIP-seq libraries from complex plant material and thereby acquire representative sequencing data.