Joint Office undertakes the implementation of the Ecclesiastical Entities (Properties) Act. It is led by the Head of Joint Office who is appointed with agreement between Government of Malta and the Holy See. Joint Office is composed of three main sections:
Registration Section which coordinates and submits applications for registration of property (on behalf of Government of Malta) at the Land Registry Agency.

Reconciliation & Migration Section which is responsible for verifications and research regarding properties included in the Act, raising of correction sheets for the approval of the Control Committee, reconciliation of the capitalised value of property and the migration of files to the Lands Authority. The section also coordinates the issue of Bonds as per Articles 6 & 7 of the Act, and administers the 2019 TDD Redemption Scheme (redemption eventually performed by the Lands Authority).

Finance & Administration Section which operates a supporting function for all Joint Office operations. Functions include Finances, Human Resource Management, Payroll, Procurement Registry and Operations.