An opening concert will mark the start of the six month presidency, where Commission President Jean-Claude Juncker will deliver a keynote speech, along with Estonian Prime Minister Jüri Ratas and Council President Donald Tusk.
Estonia formally takes over the rotating presidency from Malta on Saturday and will steer the EU agenda until the end of the year.
On Thursday, Commission Vice-President Andrus Ansip held a citizens' dialogue in Tallinn together with Estonian President Kersti Kaljulaid.
On Friday, Juncker and his colleagues will discuss with the Estonian government the challenges and priorities for the EU for the next six months.
A Commission source said the meetings will be organised in four clusters: external relations, security, migration and justice; energy and climate policy, transport and rural development; growth, competitiveness, the internal market, digital single market and trade; and the EU budget, the economic and monetary union and the social agenda.
Estonia will hold the presidency for the first time since its accession to the European Union in 2004.