The Operation Wallacea Trust was established in 2000 in the UK in order to support activities that could directly contribute towards the conservation of biodiversity in the areas in which Operation Wallacea is working. The Trust is a UK registered charity (Charity number 1078362) which is entirely independent of Operation Wallacea and is chaired by the Rt. Hon Kenneth Clarke QC MP. The Trustees are senior biodiversity and conservation management academics (Professor Aubrey Manning, Professor Ian Swingland, Professor Jules Pretty, Dr Nigel Dunstone) and the business sector (Dr Ben Vivian, Martin Suthers and Simon Notley).

Funding to support the admin costs of the Trust in the UK are provided by Operation Wallacea and other donations from the business community. The Trust can therefore ensure that 100% of the funds raised to support overseas projects are actually spent in those countries.

Currently, the Operation Wallacea Trust is working in the following areas:
 
  Conservation of the Lambusango forests in central Buton Island, Indonesia.
  Protection of the reefs and establishment of a sustainable fishery around Kaledupa Island in the Wakatobi National Park, Indonesia.
Environmental training in Government departments in SE Sulawesi
Establishment of a best practice management scheme for the Cusuco cloud forest National Park, Honduras.
  Economic alternatives for Honduran Coastal Communities adjacent to the Cayos Cochinos Marine Protected Area.
Developing environmental proposals for the St Katherine Protectorate in Sinai, Egypt

In Indonesia the Trust has a registered Yayasan (NGO) that is run by Dr Edi Purwanto. This Yayasan was originally created as the vehicle to manage the funds for the GEF/World Bank Lambusango project, but it has now expanded to administer the funds received from the Darwin Initiative, for establishing a sustainable reef fishery on Kaledupa and from the World Bank for environmental training of government staff throughout SE Sulawesi. This mix of a self-funded UK based management Trust with influential politicians, academics and business Trustees and a small management team working in the host country works well because there are funding opportunities available at both international and national level and these can be accessed by relevant personnel either in the UK Trust or in the Indonesian based Yayasan. In addition the main principle of the way the Trust and Yayasan manage projects is to ensure that businesses are developed where there is a direct link to conservation of the forests or reefs.