Embryonic stem cells repress retroviral infection through transcriptional silencing of proviral DNAs. We characterized two distinct mechanisms of silencing in embryonic mouse cells infected by Moloney murine leukaemia virus (MLV): a highly efficient one targeting the proline transfer RNA primer‐binding site (PBSpro), and a less efficient one operating independently of the PBS. Rare virus‐expressing populations were isolated, and the timing and efficiency of establishment of silencing were determined. Superinfection of the selected virus‐expressing cells with a second virus carrying a distinguishable reporter revealed that the PBSpro‐directed silencing was still largely intact, whereas the PBS‐independent silencing was partially reduced. The timing and stability of silencing, and the associated chromatin modifications on newly established and endogenous proviruses were determined. The results indicate that epigenetic mechanisms with different specificity and efficiency are used to silence the exogenous retroviral sequences in embryonic cells.