Immunogenicity of allogeneic human induced pluripotent stem cell (hiPSC)-derived transplants limits their applicability in regenerative medicine. Selecting human leukocyte antigen (HLA)-homozygous hiPSC lines could be a mitigation strategy and haplo-matching would profoundly expand the number of potential recipients. Here we show deep immune-phenotyping of hiPSC-derived cardiomyocytes (iPS-CM) differentiated from four independent iPSC lines in three centers under chemically defined conditions. Broad immunophenotyping with 354 antibodies revealed differential expression of 101 immune-related molecules between iPS-CM and the parental hiPSC lines. We selected 54 key immune markers for deep immune-phenotyping by spectral flow cytometry at the single-cell level. We found that HLA-homozygous iPSCMs exhibit an overall stable immune-phenotype across HLA-homozygous and heterozygous hiPSC lines indicating a robust differentiation process. The data indicate generally stable immune-phenotype of iPS-CM produced at three different sites and support feasibility of monitoring iPS-CM identity by spectral flow cytometry.