Background and aim The COVID-19 pandemic has left a lasting imprint on immune function, particularly in the elderly—a population already vulnerable to immunosenescence. While acute and long-COVID immune responses have been widely studied, the long-term apoptotic behavior of peripheral blood mononuclear cells (PBMCs) remains underexplored. This study aims to investigate the legacy of SARS-CoV-2 on PBMC apoptosis in elderly individuals during the post-COVID era, shedding light on potential persistent immune dysregulation. Materials and methods In this cross-sectional study, PBMCs were isolated from peripheral blood samples of elderly individuals (> 65 years old) with a documented history of COVID-19 infection at least six months prior. Using multiparametric flow cytometry, we quantified early and late apoptosis markers (Annexin V/PI), mitochondrial membrane potential disruption (ΔΨm), and expression of pro-apoptotic (Bax, Caspase-3) and anti-apoptotic (Bcl-2) proteins. Statistical analyses were performed to assess intergroup differences and correlations with clinical history. This study was conducted in 2025. Results Elderly post-COVID individuals exhibited a significantly elevated proportion of apoptotic PBMCs compared to controls (p < 0.01), particularly within the CD4 + and CD8 + T-cell subsets. Mitochondrial depolarization and increased Bax/Bcl-2 ratios indicated a shift toward intrinsic apoptotic pathways. Caspase-3 activation was also heightened in the post-COVID group. Notably, apoptotic burden correlated with time since infection and severity of initial illness. Discussion Our findings suggest a prolonged apoptotic signature in the immune cells of elderly individuals following recovery from COVID-19. These alterations may reflect a sustained immune exhaustion or maladaptive remodeling of lymphocyte populations, potentially contributing to impaired immunosurveillance and increased vulnerability to secondary infections or chronic inflammatory conditions. Conclusion COVID-19 may cast a long immunological shadow in the elderly, with persistent PBMC apoptosis representing a novel facet of post-viral immune dysregulation. Flow cytometry reveals a unique apoptotic phenotype that could serve as a biomarker for long-term immune health and guide post-pandemic clinical management strategies for aging populations.