Phi Iota Alpha history can be traced to the development of the Union Hispano-Americana (UHA) at Rensselaer Polytechnic Institute in the late 1800s. UHA was inspired by the work of five great Latin American leaders, today known by the fraternity as "The Pillars." UHA was finalized in 1898 and its main goal was to provide a cultural environment for students from Latin America and Spain. This was the first official association of Latin American students established in the United States.

In 1916, Pi Delta Phi fraternity was founded in Massachusetts Institute of Technology with similar goals and interests as UHA. In 1918, Pi Delta Phi decided to expand among various American Universities. To accomplish this goal, it established communications with Phi Lambda Alpha, a fraternity with a similar vision located at the University of South California. Subsequently, these two organizations and the UHA united in June 1921 under the name of Phi Lambda Alpha. During this time, Sigma Iota Fraternity or "La Sigma" was working to establish itself in universities across the southern United States. Sigma Iota was started in 1904 as Sociedad Hispano Americana at Louisiana State University and strove to assist fellow Latin American students academically.

In 1925, very important negotiations began between "La Sigma" and Phi Lambda Alpha. History was made when these two organizations unified in December 26,1931 and became Phi Iota Alpha Fraternity Inc., with chapters in the United States, Latin America, and Europe. In June 1932, the organizational system of Phi Iota Alpha was improved and the "Union Latino Americana" was introduced. Under the ULA system, each one of the Latin American countries constituted a zone of the union. Phi Iota Alpha constituted the zone for the United States. By 1938, there were active zones in Puerto Rico, Mexico, Cuba, Guatemala, and Belgium. Unfortunately, World War II interrupted the activities of UHA causing many chapters and zones to deteriorate. In 1945, the activities resumed and active zones were organized in Peru and Chile. The 60s proved to be a troubling time for Phi Iota Alpha because of the "me" generation and the Vietnam War.

Undergraduate activity was low among Phi Iota Alpha and other Greek organizations. The last active chapter of Phi Iota Alpha closed its doors at Rensselaer Polytechnic Institute, in 1973. However, the graduate members continued the pursuit of obtaining successful careers and made a point of maintaining communication and pursuing the development of Phi I A. Interest in Phi Iota Alpha was renewed in 1984 at Rensselaer Polytechnic Institute. In April 1984, the re-founders held the first organizational meeting regarding the Latino concerns fraternity. By the end of the year, Phi Iota Alpha's 2nd generation was born. Since then, Phi Iota Alpha has re-founded chapters and started new chapters, with the hopes of expanding the richness of Latino culture across the nation