BCI strives for a well balanced financial support avoiding any financial dominance of one specific stakeholder group.

From 2007 to 2009, the BCI has been funded by the Swedish International Development Agency (Sida), the State Secretariat for Economic Affairs (SECO) of the Swiss Confederation, Interchurch Organisation for Development Co-operation (ICCO). 

The BCI is currently funded by its members , WWF-Sweden and the Better Cotton Fast Track Programme.