The TRTA II programme is being implemented via joint management mode under a Contribution Agreement between the European Commission and UNIDO. For the European Commission, centralized direct management is undertaken by the EC Delegation to Pakistan. The Government of Pakistan is represented by the Ministry of Commerce, which is the lead institution for the beneficiary.

The overall management of the programme is guided by a Programme Steering Committee (PSC), jointly chaired by the EC Delegation to Pakistan and MoC. The UNIDO/TRTA Programme Management Office (PMO) acts as the Secretariat to the PSC.