Empire Logistics emerged out of discussions at The Los Angeles Public School during the 2009 University of California student protests. Several UC Riverside instructors and students present at those meetings and events began meeting independently in an attempt to connect the student movement with labor initiatives in Riverside and throughout the Inland Empire region. The Inland Empire, as a major logistics corridor, was an area of Southern California that was hit hardest by the subprime mortgage crisis of 2008, the resulting recession, and the accompanying slowdown in goods movement. In fact, one of the reasons for the severity of the crash in this region is the structural link between the housing boom and the goods movement industry. An astonishing 40-plus percent of all the goods that enter the United States move through the Inland Empire, making it one of the largest distributions hubs in the country.

Initial class projects initiated by EL at Cal Poly, Pitzer College and UC Riverside focused on Mira Loma, a census-designated area that contains the highest density of warehouses in the United States. These warehouse house goods for all of the major U.S. retailers (such as Walmart, Target, Walgreens, Home Depot, etc) in massive distribution centers before moving them to their retail outlets all over the country.

In 2011, the project re-located to the San Francisco Bay area—connecting with the Global Supply Chain study group already meeting at The Public School, San Francisco. In 2014, programmers contributed a comprehensive supply chain infrastructure map, with detailed railroad and port data gleaned from available databases and retail warehouse data compiled by EL researchers. An Empire Logistics conference was held at the Los Angeles Public School in 2014.