Indiana, like some of his fellow artists, scavenged the area's abandoned warehouses for materials, creating sculptural assemblages from old wooden beams, rusted metal wheels, and other remnants of the shipping trade that had thrived in Coenties Slip. While he created hanging works such as Jeanne d'Arc (1960-62) and Wall of China (1960-61), the majority were freestanding constructions which Indiana called "herms" after the sculptures that served as boundary markers at crossroads in ancient Greece and Rome. The discovery of nineteenth-century brass stencils led to the incorporation of brightly colored numbers and short emotionally charged words into these sculptures as well as canvases, and became the basis of his new painterly vocabulary.

Indiana quickly gained repute as one of the most creative artists of his generation, and was featured in influential New York shows such as New Media-New Forms at the Martha Jackson Gallery (1960), Art of Assemblage at the Museum of Modern Art (1961), and the International Exhibition of the New Realists at the Sidney Janis Gallery (1962). In 1961, the Museum of Modern Art acquired The American Dream, I (1960-61), the first in a series of paintings exploring the illusory American Dream, establishing Indiana as one of the most significant members of the new generation of Pop artists who were eclipsing the prominent painters of the New York School.

Although acknowledged as a leader of Pop, Indiana distinguished himself from his Pop peers by addressing important social and political issues and incorporating profound historical and literary references into his works. American literary references appear in paintings such as The Calumet (1961) and Melville (1961), exhibited in 1962 in Indiana's first New York solo exhibition, held at Eleanor Ward's Stable Gallery. In 1964 Indiana accepted Philip Johnson's invitation to design a new work for the New York State Pavilion at the New York World's Fair, creating a twenty-foot EAT sign composed of flashing lights, and collaborated with Andy Warhol on the film Eat, a silent portrait of Indiana eating a mushroom in his Coenties Slip studio. His first European solo exhibition took place in 1966 at Galerie Schmela in Düsseldorf, Germany, and featured his Number paintings (1964-65), a series of works on a theme that he has explored in various formats throughout his career.

1966 marked a turning point in Indiana's career with the success of his LOVE image, which had been featured in a solo exhibition at the Stable Gallery.  The word love, a theme central to Indiana's work, first appeared in the painting 4-Star Love (1961). Love was a subject of great spiritual significance for the artist, illustrated by the painting Love Is God (1964), which was inspired by an inscription in the Christian Science churches he attended in his youth.  Initially experimenting with a composition of stacked letters in a series of 1964 rubbings, Indiana subsequently turned this inventive design, a formal departure from his previous works, into different hard-edged color variations on canvas.  Indiana's LOVE, selected by the Museum of Modern Art in 1965 for its Christmas card, quickly permeated wider popular culture, and was adopted as an emblem of the "Love Generation." Appearing on a best-selling United States Postal Service stamp (1973) and reproduced on countless unauthorized products, the proliferation of the image led, on one hand, to negative criticism and incorrect assumptions of the artist as a sell-out. However, the image's popularity more importantly emphasizes its great resonance with large and diverse audiences, and has become an icon of modern art. The universality of the subject, to which Indiana continued to return, is further evidenced by his translation of LOVE into AHAVA (Hebrew) and AMOR (Spanish).

In 1978, Indiana chose to remove himself from the New York art world. He settled on the remote island of Vinalhaven in Maine, moving into the Star of Hope, a Victorian building that had previously served as an Odd Fellows Lodge. After a period spent setting up his home and new studio, Indiana turned to themes that related to his local experience, working on a suite of eighteen large-scale paintings known as The Hartley Elegies (1989-94), inspired by the German Officer paintings of Marsden Hartley, who lived on Vinalhaven in the summer of 1938. He also used found objects to create sculptures such as Ash (1985) and Mars (1990), works that reflected his new surroundings while also making reference to his past, and returned to and expanded upon his seminal American Dream series, completing The Ninth American Dream in 2001.