Noboa has been actively involved in politics, unsuccessfully running for the office of President of Ecuador in 1998, 2002, 2006, 2009 and 2013. In 2007, however, he was elected national assemblyman.In 2013 Noboa ran for office for the fifth time unsuccessfully. Ecuadorian Presidential Elections 
In 1997, already owning 24% of Bonita Bananas, Noboa purchased another 25% of the shares, the holding company for the family business. Presently, he runs the Noboa Group of Companies and Noboa Corporation, with more than 110 companies in Ecuador and around the world, including branch offices in United States, Antwerp, Rome, Japan, Argentina, and New Zealand.
Some of Noboa's Ecuadorian companies have faced lawsuits and Servicio de Rentas Internas claims. The banana exporting company also has been audited by international organisations due to child labor issues and strike conflicts.
Noboa's major company in Ecuador, Exportadora Bananera Noboa, faced as of February 2009, an assessment of three hundred million dollars (Ecuador was dollarized in 2000) imposed by the governmental revenue service of Ecuador, the SRI. A representative of TP Consulting, an independent audit firm, stated that what is in question is the price for a crate of bananas: that which the SRI has fixed is a number above that determined by other parts of the government (the Ecuadorian banana business is regulated by the government which sets prices paid to producers for bananas, the cost of exportation and the referential FOB price.). The representatives of Bananera Noboa have stated that exportation prices were within the range of prices of exportation of other exporters, according to information from the Central Bank of Ecuador. The audit, undertaken by TP Consulting (who were contracted to carry out a study of the transfer prices of Bananera Noboa), revealed an amount to be paid of US $139,949.00. As of 2011, Bananera Noboa is still facing charges from the SRI, but the legal representatives of the Company state that the company ‘Is not Bankrupt’.
A judge in New York has recommended a $6.96m default judgment against Alvaro Noboa in NYKCool’s long hunt for payment from the empire of the Ecuadorian banana baron.
If Magistrate Judge Andre Peck’s recommendation is approved by the higher ranking jurist overseeing the lawsuit, it will follow a string of such judgments against companies alleged to be under Noboa’s control. All but one of the judgments has gone unpaid.
NYKCool, the Stockholm-based subsidiary of Japan’s NYK Line, has been seeking payment of a 2011 arbitration award for $8.79m, plus costs, over a collapsed contract of affreightment (COA) with companies associated with Noboa, who controls the Bonita Banana brand and who was placed fifth in last year’s Ecuadorian presidential elections.