He was president of the country between 2000 and 2003 following the collapse of Mahuad’s government. Noboa was the President of Banco Popular when he participated in a compromising meeting due to the nature of the resolutions that were passed. Bajo su gobierno, el Congreso aprobó la nueva ley bancaria, impulsada por algunos de los causantes de la crisis financiera. Under his presidency, Congress approved the new banking law which was driven by some of the causes of the financial crisis. His wife is the sister of the former owner of the bankrupted Banco Union, Roberto Baquerizo Valenzuela. Nathalie Cely was also a part of that bank and is now the Ecuadorean Ambassador in the U.S.

Noboa acknowledged in a letter of December 2001 addressed to the President of the National Congress, Jose Cordero that the reform of the General Law of the System of Financial Institutions that was to become law of the land upon his signature was clearly illegal and had “clear targets.” However, he refused to assume the political cost of the veto; He stated that "there were superior values to those of the state" and then entrusted himself to God and country so that he could be judged by them. When the country did judge him, in an attempt to save himself Noboa cloaked himself in amnesty declaring that he was being politically persecuted.

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