Following the 2000 presidential election, he took an ardent secularist approach on issues such as the headscarf, holding the view that secularism in Turkey was under threat.

A quarrel between Sezer and Prime Minister Bülent Ecevit in 2001 led to a financial meltdown, attributed to the weakness of the coalition government as well as to the large debt owed to the International Monetary Fund.

The landslide victory of the conservative Islamist Justice and Development Party (AKP) in the 2002 general election led to strong opposition from President Sezer, who vetoed several proposed laws and referred others to the Constitutional Court.

On 21 February 2001, during a quarrel in a National Security Council meeting, he threw the constitutional code book at Prime Minister Bülent Ecevit.

Others claimed that the rapid reforms called for by the accession negotiations with the European Union and Turkey's strong ties with the International Monetary Fund caused the crisis.

[12] During the 2014 presidential election, won by Erdoğan, Sezer openly refused to vote, citing the lack of a secularist candidate as his reason.