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Introduction Membranoproliferative glomerulonephritis (MPGN) represents a histologic pattern of glomerular injury which may be due to several etiologies. Few studies have comprehensively analyzed the recurrence of MPGN according to the current classification system. Methods We collected a multicenter, retrospective cohort of 220 kidney graft recipients with biopsy-proven native kidney disease due to MPGN between 1981–2021 in 11 hospitals. Demographic, clinical and histologic parameters of prognostic interest were collected. The main outcomes were time to kidney failure, time to recurrence of MPGN, and disease remission after recurrence. Results The study group included 34 complement-mediated and 186 immune complex-mediated MPGN. Eighty-one patients (37%) reached kidney failure in a median follow-up of 79 months. The main predictors of this event were the development of rejection episodes, and disease recurrence. Fifty-four patients (25%) had a disease recurrence in a median of 16 months after kidney transplantation. The incidence of recurrence was higher in patients with dysproteinemia (67%) and complement-mediated MPGN(62%). In the multivariable model, complement-mediated MPGN emerged as a predictor of recurrence. Thirty-three patients reached kidney failure after recurrence. The main determinants of no remission were: early time to recurrence (<15 months), eGFR < 30 ml/min/1.73m2 and serum albumin < 3.5 g/dl at the time of recurrence. Conclusions One-fourth of patients with native kidney disease due to MPGN developed clinical recurrence in the allograft, especially in cases with complement-mediated disease or in those associated with dysproteinemia. The kidney outcomes of disease recurrence with currently available therapies are heterogeneous and thus, more effective and individualized therapies are needed.

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