The development of hematopoietic cell lineages is a highly complex process governed by a delicate interplay of various transcription factors. The expression of these factors is influenced, in part, by epigenetic signatures that define each stage of cell differentiation. In particular, the formation of B lymphocytes depends on the sequential silencing of stemness genes and the balanced expression of interdependent transcription factors, along with DNA rearrangement. We have investigated the impact of Dido3 deficiency, a protein involved in chromatin status readout, on B cell differentiation within the hematopoietic compartment of mice. Our findings revealed significant impairments in the successive stages of B cell development. The absence of Dido3 resulted in remarkable alterations in the expression of essential transcription factors and differentiation markers, which are crucial for orchestrating the differentiation process. Additionally, the somatic recombination process, responsible for generation of antigen receptor diversity, was also adversely affected. These observations highlight the vital role of epigenetic regulation, particularly the involvement of Dido3, in ensuring proper B cell differentiation. This study reveals new mechanisms underlying disruptive alterations, deepening our understanding of hematopoiesis and may potentially lead to insights that aid in the development of therapeutic interventions for disorders involving aberrant B cell development.