Summary Reduced immunosuppression during BKV‐DNAemia has been associated with T‐cell mediated rejection (TCMR), de novo donor‐specific antibodies (DSA) and antibody‐mediated rejection (ABMR). Intravenous immunoglobulins (IVIG) may reduce alloimmunity. We studied 860 kidney transplant recipients (KTRs) for the development of BKV‐DNAuria and BKV‐DNAemia (low‐level <10 000 IE/ml, high‐level >10 000 IE/ml). 52/131 KTRs with high‐level BKV‐DNAemia received IVIG. The HLA‐related immunological risk was stratified by the Predicted Indirectly Recognizable HLA Epitopes (PIRCHE) algorithm. BKV‐DNAuria only was observed in 86 KTRs (10.0%), low‐level BKV‐DNAemia in 180 KTRs (20.9%) and high‐level BKV‐DNAemia in 131 KTRs (15.2%). KTRs with low‐level BKV‐DNAemia showed significantly less TCMR compared to KTRs with high‐level BKV‐DNAemia (5.2% vs. 25.5%; P < 0.001) and no BKV‐replication (13.2%; P = 0.014), lowest rates of de novo DSA (21.3%), ABMR (9.2%) and flattest glomerular filtration rate (GFR) slope (−0.8 ml/min). KTRs with low‐level BKV‐DNAemia showed significantly higher median (interquartile range) total PIRCHE if they developed TCMR [100.22 (72.6) vs. 69.52 (49.97); P = 0.020] or ABMR [128.86 (52.99) vs. 69.52 (49.96); P = 0.005]. Administration of IVIG did not shorten duration of BKV‐DNAemia (P = 0.798) or reduce TCMR, de novo DSA and ABMR (P > 0.05). KTRs with low‐level BKV‐DNAemia showed best protection against alloimmunity, with a high number of PIRCHE co‐determining the remaining risk. The administration of IVIG, however, was not beneficial in reducing alloimmunity.