The Church Council is the highest authority and policymaking body of the HCC. It consists of representatives from the local congregations, which meets once in a year. Every congregation sends delegates according to their numerical strengths.

The Executive Committee is elected by the Church Council to carry out all the responsibilities on behalf of the Church Council.

The Project Committee of HCC is overall responsible for all interventions within the program carried out by the church. The committee consists of 7 members.

The responsibility of the committee is to receive applications for scholarships from the deserving candidates. The committee, after detailed deliberation and verification approves scholarships.

There are 101 ordained pastors, 6 ordained women pastors, 40 evangelists and 6 Bible Women. The current staff strength of HCC is 245 located in all its programme areas and Head Quarter at Pune.

Covenant Social Service (CSS)

Covenant Social Service (CSS) is a development wing under HCC committed to serve the poor and marginalised people of India through evangelistic literacy; medical, educational & welfare work. CSS modified its approach from welfare oriented to integrated community based development. The locations where CSS works are slums, semi urban or villages. CSS reaches out to the needy communities in eight states and one union territory of India.

St. Luke's Medical Society is a separate wing of HCC headed by Board Members. The two health centers at Nannaj in Maharashtra and Aurad in Karnataka are totally committed to provide health services to the poor and marginalized.

Solapur Well Service is an independent wing under HCC serving to provide safe drinking water to poor and marginalized of drought prone and disaster affected areas, through drilling tube wells and repairing old tube wells.