Lilly helped improve the company's business processes to increase its efficiency, laid the groundwork for its personnel guidelines, and formed its sales research department.

In 1937 Joe, his brother, and their father, founded the Lilly Endowment, which remains as one of the largest charitable foundations in the world.

Cape Cod's Heritage Museums and Gardens was established in his honor in Sandwich, Massachusetts, and holds some of Lilly's other collections.

[5][6] He continued his education with a two-year course at the University of Michigan College of Pharmacy, which he completed in 1914, and then returned to Indianapolis to join the family business.

Following his enlistment in the U.S. Army during World War I, when he served in France as an officer in the medical supply service, Lilly returned to the family business in Indianapolis, where he spent the remainder of his career.

[7] In the late 1920s Lilly and his brother, Eli, established a Planning Department and developed improvements to the company's hiring procedures, employee bonus incentives, working conditions, and efficiency efforts.

[13] He was known for his philanthropic activities, as well as his collections of rare books and manuscripts, gold coins, antique weaponry, stamps, works of art, and military miniatures.

As the company's stock value increased, the Lilly Endowment became one of the largest private foundations in the United States.

His collection was especially strong in American and British literary classics, as well as the history of science and medicine and Americana.

[19][20] Lilly eventually donated to IU more than 20,000 books and 17,000 manuscripts, in addition to more than fifty oil paintings and 300 prints.

[21][22] In the late 1950s, Lilly provided the funding for construction of a new special collections library on the IU Bloomington campus.

His daughter donated an estimated $800 million during her lifetime to numerous charitable organizations and non-profit institutions, most of them in Indiana and in Indianapolis.

[25] [26] Eli (Ted) Lilly II, Josiah III's son and Joe Jr.'s grandson, maintains a low profile in the Indianapolis area.

His son joined the family business in 1939 and became superintendent of its Kentucky Avenue plant after serving in the military during World War II; however, he resigned from the company in 1948 and did not succeed his father as president.

[11][24] In December 1932, Lilly purchased Oldfields, a French chateau-style home with landscaped gardens, from Hugh McKennan Landon, an Indianapolis businessman.

In 1936 Lilly moved his collection of rare books and manuscripts from his home to the library he had built on the property, which also included a lodge.

The Lilly family purchase adjoining property to expand the estate, known as Twin Oaks, to 22 acres (8.9 hectares).