QCI is governed by a Council of 31 members with equal representations of government, industry and consumers. Chairman of QCI is appointed by the Prime Minister's office on recommendation of the government and industry.

Council is the apex level body responsible for formulating the strategy, general policy, constitution and monitoring of various components of QCI including the accreditation boards with objective to ensure transparent and credible accreditation system. The Council through a Governing Body monitors the progress of activities and appeal mechanisms set by the respective boards.

QCI functions through the executive bodies (boards / committees) that implement the strategy, policy and operational guidelines set by the Quality Council of India with a view to achieve international acceptance and recognition of various components including the accreditation systems.

Each Board has a Chairman nominated by the QCI Chairman. The Boards comprise of representative volunteer group of stakeholders who guide and pursue the activities and progress of the respective Boards.