Genome-wide chromatin profiling is a robust approach to define the mechanisms underlying epigenetic gene regulation. Among the available techniques, Cleavage Under Targets and Tagmentation (CUT&Tag) has emerged as a highly efficient method for profiling diverse chromatin components and modifications. Its appeal lies in the simplicity of the experimental steps, the minimal input requirements, and the generation of reproducible high-quality data. Here, we provide a detailed guide to a series of optimized spike-in CUT&Tag protocols tailored for quantitative epigenomic profiling of mouse germ cells. We illustrate this application of the methodology using our recent comprehensive study of adult mouse spermatogonial cells as an example. The experimental process involves fluorescence-activated cell sorting to isolate adult spermatogonial cells, the implementation of a spike-in CUT&Tag protocol to generate sequencing libraries, and the subsequent bioinformatics analysis of the resulting sequencing data. This framework provides a versatile approach to quantitative epigenomic analysis, extending far beyond the specific context of male germ cells.