In 1990 The Algebra Project received more grants including the award of a MacArthur "Genius" Foundation prize to Robert Moses. As a result the organization filed for incorporation in April of 1990. Because of these grants and the support of the department head of mathematics for the Chicago school system, the Algebra Project expanded from Boston to Chicago. Shortly thereafter, Algebra Projects were initiated in Louisville, Milwaukee, Oakland, and Atlanta.

In 1991 the Algebra Project moved to its present location on Bishop Richard Allen Drive in Cambridge. New projects were begun in Indianapois, San Francisco and Los Angeles. Dave Dennis, a fellow veteran of the Civil Rights Movement, with Moses's encouragement started an Algebra Project "pilot" program in six Mississippi Delta schools.

In 1992, the Algebra project demonstrated the success of its approach in just one Boston public school where 68 percent of the children enrolled in the Algebra Project went on to ninth-grade algebra, compared with only 54 percent system wide.

In 1993 there was an Algebra Project in New York City. That same year, a more formal program in several southern cities was established as the Southern Initiative of the Algebra Project under the direction of Dave Dennis.

With the help of Moses's two sons, Omo and Tabasuri, the Young Peoples' Project was founded and formalized in 1996 with sites in Cambridge and Mississippi with the purpose of emphasizing the importance of math literacy.

In recent years, Robert Moses has focused on the development of curriculum for the Algebra Project as well as teaching algebra and geometry at Lanier High School in Jackson, Mississippi.