During hematopoiesis, lineage- and stage-specific transcription factors work in concert with chromatin modifiers to direct the differentiation of all blood cells. Here, we explored the role of KRAB-containing zinc finger proteins (KRAB-ZFPs) and their cofactor KAP1 in this process. Hematopoietic-restricted deletion of Kap1 in the mouse resulted in severe hypoproliferative anemia. Kap1-deleted erythroblasts failed to induce mitophagy-associated genes and retained mitochondria. This was due to persistent expression of microRNAs targeting mitophagy transcripts, itself secondary to a lack of repression by stage-specific KRAB-ZFPs. The KRAB/KAP1-miRNA regulatory cascade is evolutionary conserved, as it also controls mitophagy during human erythropoiesis. Thus, a multilayered transcription regulatory system is present, where protein- and RNA-based repressors are superimposed in combinatorial fashion to govern the timely triggering of an important differentiation event.