In plants, programmed cell death (PCD) is a fundamental cellular process during development that can also be triggered upon biotic and abiotic stresses. In Arabidopsis thaliana, PCD is an integral part of the differentiation process of the root cap, a specialized organ that surrounds the meristematic stem cells. The acquisition of cell death competence in lateral root cap (LRC) cells depends on the root cap-specific transcription factor ANAC033/SOMBRERO (SMB). Cell death is followed by a rapid cell-autonomous corpse clearing process on the root surface involving the senescence-associated nuclease BFN1 downstream of SMB. Based on transcriptomic datasets we observed the downregulation of BFN1 during Serendipita indica colonization in Arabidopsis, which prompted us to investigate the roles of SMB and BFN1 in fungal accommodation. We show that roots of smb3 mutants, which are deficient in root cap PCD and corpse clearance, are entirely covered by undegraded LRC cell corpses loaded with protein aggregates. The accumulation of uncleared cell corpses promotes intra- and extraradical colonization by S. indica, which in turn is sufficient to subsequently clear the cell corpses from the surface of smb3 roots. Compared to smb3, the bfn1-1 knockout mutant exhibits an attenuated corpse clearance phenotype, but still enhances colonization by S. indica. These results highlight the importance of root cap differentiation in plant-microbe interactions and show that the constant production and clearance of LRC cells represents a sophisticated physical defense mechanism to prevent microbial colonization in close proximity to meristematic stem cells. Furthermore, we propose a mechanism by which S. indica manipulates developmental PCD in Arabidopsis roots by downregulating BFN1 to promote fungal colonization through reduced clearance of dead LRC cells as a potential source of nutrients.