The implementation of the Protocol is overseen by an institutional framework bringing together a set of dedicated UK-EU committees established under the Withdrawal Agreement and a series of joint EU-UK bodies established by or as a consequence of the 1998 Belfast ‘Good Friday’ Agreement that underpins the Northern Ireland peace process; including those created under the Northern Ireland Act 1998. 

Dedicated to the implementation of the Protocol are:

• Joint Committee - the decision-making body for the Protocol
• Specialised Committee - makes recommendations regarding the functioning of the Protocol to the Joint Committee 
• Joint Consultative Working Group - forum for exchange of information and mutual consultation regarding the implementation of the Protocol

Initial meetings of each of the three bodies were held in 2020-21, but for much of 2022 the deterioration in UK-EU relations over the Protocol meant that the Joint Committee and Specialised Committee only managed to meet once and the institutional framework - with the exception of the Joint Consultative Working Group - failed to function. With the agreement of the Windsor Framework (2023), however, the European Commission and the UK Government committed to make full use of the institutional framework for the Protocol and to 'organise meetings of the relevant joint bodies on a regular basis in order to foster dialogue and engagement'.

The European Commission and the UK Government also agreed in the Windsor Framework:

• for the Specialised Committee to meet additionally in special formations (Special Body on Goods; Enhanced Coordination Mechanism on VAT and excise concerning goods)
• for the Joint Consultative Working Group to establish relevant subgroups
• to formalize and regularize engagement with stakeholders from Northern Ireland

Feeding into the work of the Specialised Committee are:

• The North-South Implementation Bodies established by the 1998 Agreement
• The North-South Ministerial Council (when active)
• Human Rights and Equality Bodies set up pursuant to the 1998 Agreement and responsible for overseeing implementation of Article 2 of the Protocol