The bank was originally called La Filantrópica (The Philanthropist). Under the leadership of Pedro Isaías Barquet, La Filantrópica promoted the development of small industry, commerce, and agriculture, and became established as a strong and solvent financial institution. At the time of Isaías Barquet's death in 1960, the family decided to save the bank and inject it with capital.
It was acquired in 1960 by the Isaías Group (Grupo Isaías), who decided to change its name to Filanbanco. They injected capital into the bank, aiming to provide Guayaquil with a bank that would further the expansion of the commercial and agricultural sector of the Littoral Region, whose trade in products like bananas and cacao was booming.
The bank belonged to the Isaías family for three generations.
In 1998, during the Ecuadorian financial crisis, the bank faced a liquidity crisis. It was sold to the government of Ecuador that year. It was merged by the government with the bank La Previsora in an operation questioned because Filanbank had to bear La Previsora's huge losses. Once in control of the Ecuadorian government, it was used as a bank of banks to allocate assets to provide liquidity to troubled banks in 2000 and 2001, during the banking crisis. Filanbanco closed its doors definitively in July 2001.
The state was conducting an investigation into the administration of the Isaías brothers. The Deposit Guarantee Agency (Agencia de Garantía de Depósitos, AGD) later seized control of several companies related to the Isaias family to recover an estimated $350 million still owed in relation to the restructuring of Filanbanco.