Several studies have assessed clinical outcomes after steroid withdrawal (SW) in kidney transplant (KT) recipients, but little is known about its potential impact on lymphocyte subpopulations. We designed a prospective study to evaluate the long-term impact of SW in 19 KT recipients compared to 16 KT recipients without changes in immunosuppression (steroid maintenance, SM). We assessed renal function, presence of HLA antibodies and peripheral blood lymphocyte subsets at time of inclusion, and 3, 12 and 24 months later. The immunophenotype of 20 healthy subjects was also analyzed. Serum creatinine and proteinuria remained stable in SW and SM patients. SW did not associate with generation of de novo donor-specific antibodies. SW patients showed decreases in T-lymphocytes (p < 0.001), and in the CD4+ T cell subpopulation (p = 0.046). The proportion of B-lymphocytes (p = 0.017), and both naïve and transitional B cells increased compared to SM patients (p < 0.001). Changes in B cell subsets were detected 3 months after SW and persisted for 24 months. No changes were observed in NK cells related to steroid withdrawal. SW patients displayed significant changes in peripheral T and B cell subsets, transitioning to the phenotype detected in healthy subjects. This may be considered as a maintained positive effect of SW previously unnoticed.