IOTA was established in 1996 in the 3rd Conference of Central and Eastern European and Baltic Countries’ Tax Administrations held in Warsaw (28 –30 October). The setting up of the Organisation took place in December, with the launching of the Secretariat and the nomination of the first President and Executive Secretary. The creation of the Charter of IOTA and the formation of the Executive Council, one of the main decision making bodies of the organisation, were among the milestones that eventually paved the way for the organisation of the annual work programme. The Secretariat became operational as of from 1 March 1997, with 7 founding members.

At the 1st General Assembly (29 September – 2 October, 1997) the Seat Agreement was signed between IOTA and the Government of the Republic of Hungary. The first Executive Secretary of IOTA was Mr. Jacques Carre from the French Tax Administration.

IOTA in the initial years successfully concentrated on profile building and establishing credibility on the international scene.  A common understanding was also reached that IOTA represented the members’ mutual interest by providing a forum for the exchange of experience and assistance for the modernisation of tax administrations in Central and Eastern Europe, especially in the context of the enlargement of the European Union. By the joining of the EU of several member states the profile of IOTA has shifted from assistance in modernisation to share of experiences and best practices.

In the past years IOTA has significantly widened its membership and its international activity. IOTA has 43 full members and 1 associate member today. IOTA has developed cooperation with various international organisations which provide technical assistance to tax administrations worldwide. Memoranda of Understanding have been signed with CIAT, the European Commission and OECD.

The decisions about accession of member states were made in the following General Assemblies:

1996 7 founding members(Bulgaria, Czech Republic, Hungary, Latvia, Lithuania, Poland, Slovakia)
1997 3 new full members (Albania, Former Yugoslav Republic of Macedonia and Slovenia) and 5 associate members)
1998 3 new members (Romania as a full member and Denmark and Germany as associates).
1999 4 new members: Estonia as a full member and Austria, Belgium and Italy as associate.
2001 Croatia and Moldova became members, Finland and Sweden associate members. The membership grew to 14 full members and 12 associate members.
2002 Azerbaijan, Germany and Serbia became full members, and Iceland, Norway and Switzerland associate members of the Organisation. Membership had now grown to 17 full members and 15 associate members.
2003 The United Kingdom and Montenegro were accepted as full members and Ireland and Ukraine (as from the year 2004) joined as associate members.
2004 France, Georgia and Ireland and the two entities of Bosnia and Herzegovina were accepted as full members. At this time membership rose to 24 full members and 13 associate members.
2005 6 former associate members decided to become full member: the Netherlands (with immediate effect), Belgium, Finland, Norway, Spain and Sweden from 2006. 
2006 Full membership of Austria, Cyprus, Denmark, Greece, Iceland, Italy, Malta, Switzerland and Ukraine was accepted, making the membership 38
2007 The IOTA membership was increased by acceptance of the applications of the Indirect Tax Authorities from Bosnia and Herzegovina (with immediate effect), the Tax Administration from Portugal (as from 1 January 2008) and the Tax Administration from Jordan (associate membership also from 1 January 2008).
2008 The members accepted the application for immediate full membership to the Organisation by the Tax Administrations of Belarus and application for associate membership to the Organisation by the Tax Administration of Kazakhstan, with effect from 1 January 2009.
2009 The members accepted the application for immediate full membership to the Organisation by the Tax Administration of Luxembourg.
2010 The members accepted the application for full membership to the Organisation of the State Revenue Committee of the Government of the Republic of Armenia and the Federal Tax Service of the Russian Federation with effect from 1 January 2011.
2011 The members accepted the application for immediate full membership to the Organisation of the Fiscal Authority of Liechtenstein.
2016 Liechtenstein terminated its membership from 1 November
2017 Iceland terminated its membership from 1 May
2021 The National Tax Service of South Korea became an associate member from 1st July
2022 The 26th General Assembly accepted the application of the Iceland Revenue and Customs for Full Membership in IOTA which entered into effect on 29 June 2022. The Members also decided on the “continued suspension” of Russia and Belarus in all technical and administrative activities of IOTA until further notice.
2023 2023 The 27th General Assembly decided on the termination of the memberships of the Federal Tax Service of Russia and the Ministry of Taxes and Duties of the Republic of Belarus in the Intra-European Organisation of Tax Administrations (IOTA). The termination of membership resulted from an absolute majority vote of IOTA members and came into effect on 27 June 2023.