The intricate orchestration of gene expression plays an integral role in the development of immune cells. The transcription factor PU.1 is a crucial regulator in hematopoietic development and the function of granulocytes. In this study, we delve into the regulatory mechanisms underlying PU.1's impact on chromatin architecture in mouse granulocytes using multi-omics. We employed RNA sequencing to decipher transcriptome changes associated with PU.1 loss, chromatin immunoprecipitation to unravel PU.1 DNA binding events, and in situ Hi-C to explore the genome organization in a PU.1 null context. Notably, loss of PU.1 leads to a rewiring of late granulocyte identity and emergence of early progenitor markers observed in both RNA-seq and flow cytometry. Furthermore, this shift in cell profile is accompanied by changes to chromatin architecture, shedding light on the role of genome organisation in granulocyte development. Our findings illuminate the important dynamic between genome organisation and cell identity.