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A separate protocol linked to the treaty led to the creation of the euro, and introduced the Three pillars of the European Union (the European Communities pillar, the Common Foreign and Security Policy or CFSP pillar, and the Justice and Home Affairs pillar). The CFSP pillar was built on the foundation of European Political Cooperation (EPC), but brought it under a treaty and extended it. The JHA pillar introduced cooperation in law enforcement, criminal justice, civil judicial matters, and asylum and immigration. Originally, the European Community (EC) dealt mainly with economic, social and trade matters. The European Commission and the European Court of Justice, both operationally independent from the national governments, although appointed by them, had a lot of power within the system. The European Parliament, which was directly elected by the citizens of the EC member states, also had some power. The Governments retained the most power in the Council of Ministers, but since the mid-1980s had increasingly been taking decisions through qualified majority votes (about 71% of the votes). This system was called the Community method, or supranationalism, as institutions not directly controlled by the governments wielded significant power, and members could have decisions they disagreed with imposed upon them through majority votes.

It was desired to add competencies in foreign policy, military and criminal matters to the European Community. However, many member states considered that these areas were too sensitive to be managed by the mechanisms of the European Community, and that the power of governments in relation to these areas had to be stronger than the powers of governments in the European Community. That is, an intergovernmental, as opposed to supranational, system would have to be used. Other member states feared that this might threaten the power of the independent supranational institutions (the European Commission, European Court of Justice and European Parliament) in relation to the economic matters then dealt with by the European Community. The three pillar structure was then developed to isolate the traditional Community responsibilities in the area of the economy (the Community Pillar) from the new competencies in the areas of foreign policy and military matters (the CFSP pillar) and criminal matters (the JHA pillar). The Maastricht treaty created also the position of the Ombudsman.