DEEP Malaysia operates as a registered organisation, officially known as Pertubuhan Dialog, Empati, Ekologi dan Perdamaian.
It was formally registered by the Malaysian Registrar of Societies on 14 September 2018. At its inaugural AGM on 30 June 2019, the meeting endorsed the following as the office-bearers of DEEP Malaysia from 2019 to 2021.

Chair: Dr Welyne Jenom (who is also the current director of the Centre for Malaysian Indigenous Studies at University of Malaya)

Deputy Chair: Brandon Simon Scott

Secretary: Hema Letchamanan

Deputy Secretary: Qairunnisa Ahmad Noor Ridi

Treasurer: Kamal Solhaimi Fadzil

Committee Members: Abdullah Naib, Nor Arlene Tan Khalid, Philip Wong Wan Ming

Internal Auditors: Dr Lim Teck Ghee, Hishamudin Ubaidula

The Global DEEP Network Co-Directors for DEEP Malaysia are:

Dr Welyne Jenom & Hema Letchamanan