In 1979 MG Peperkoorn joined the Royal Netherlands Marechaussee (RNLM) as a conscripted officer. After following the officers training, MG Peperkoorn specialised in special police operations. In this specialism he commanded the BSB, the special security operations unit of the Royal Netherlands Marechaussee, from 1986 until 1994.
Until 2012 MG Peperkoorn held various leading positions within the RNLM. Internationally he served at NATO HQ in Brussels and became the NL member in the Management Board of Frontex, the European Agency for coordinating border management operations at the EU external borders.
In February 2012 MG Peperkoorn was appointed to Deputy Director General of the Defence Intelligence and Security Service (MIVD). In July 2014 he returned to the RNLM to contribute to the radical change to a full information led organisation and was appointed as National Tactical Commander RNLM in January 2015. On November, 1st the same year he was appointed Deputy Commander of the RNLM and subsequently promoted to Major General.