Epigenetic factors guide chromatin remodeling during cell state transitions and confer resistance to genotoxic stressors that could induce deleterious transformations. A particularly peculiar component of the epigenome with emerging roles in fine-tuning cell identity and upholding genomic stability is the structural histone variant macroH2A. Relatively little is currently known about macroH2A’s influence on overall cell developmental potency and less still is known about macroH2A’s contributions to adult stem cell identity and function in vivo. In this work, we use induced pluripotent stem cell (iPSC) reprogramming and the murine intestinal stem cell (ISC) system to model macroH2A’s overall impact on cell epigenetic identity from embryo to adult. We manipulated macroH2A content during iPSC reprogramming and concluded that macroH2A removal from somatic chromatin constitutes a mild, but present epigenetic bottleneck to pluripotency acquisition. Using epitope-tagged-macroH2A-expressing cells, we demonstrated that embryonic stem cells (ESCs) display significantly more dynamic macroH2A incorporation and turnover than fibroblasts, particularly proximal to the promoters of highly transcribed genes, concluding that macroH2A is less stably associated with ESC chromatin. In a separate study, we bred macroH2A double germline knockout (DKO) and strain-matched wildtype (WT) mice into reporter strains for ISC subpopulations, enabling us to functionally test active and reserve ISCs during homeostasis and following γ-irradiation injury. We showed that macroH2A DKO intestine is host to elevated numbers of putative reserve ISCs, suggesting that macroH2A may normally limit the size of the reserve ISC pool. We further determined that although macroH2A is unnecessary for intestinal homeostasis, macroH2A strongly bolsters the intestinal regeneration response following irradiative injury by promoting reserve ISC radioresistance. We thus conclude overall that macroH2A imposes a minor resistance to induced pluripotency, limits the size of the reserve ISC pool in adult mice and finally upholds genomic stability by providing resistance to genotoxic stress in vivo.