Lilly enlisted in the Union Army during the American Civil War and recruited a company of men to serve with him in the 18th Independent Battery Indiana Light Artillery.

Eli Lilly and Company became one of the first pharmaceutical firms of its kind to staff a dedicated research department and put into place numerous quality-assurance measures.

He turned over the management of the company to his son, Josiah K. Lilly Sr., around 1890 to allow himself more time to continue his involvement in charitable organizations and civic advancement.

Lilly helped found the Commercial Club, the forerunner to the Indianapolis Chamber of Commerce, and became the primary patron of Indiana's branch of the Charity Organization Society.

Lilly was an advocate of federal regulation of the pharmaceutical industry, and many of his suggested reforms were enacted into law in 1906, resulting in the creation of the Food and Drug Administration.

He was also among the pioneers of the concept of prescriptions, and helped form what became the common practice of giving addictive or dangerous medicines only to people who had first seen a physician.

[3] Lilly and his family were also members of the Democratic Party in his early years, but became Republicans prior to the American Civil War.

In 1858, after earning a certificate of proficiency from his apprenticeship, Lilly left the Good Samaritan to work for Israel Spencer and Sons, a wholesale and retail druggist in Lafayette, before moving to Indianapolis to take a position at the Perkins and Coons Pharmacy.

[4][10][11] The couple's son, Josiah Kirby, later called "J.K.", was born on November 18, 1861, while Eli was serving in the military during the American Civil War.

[3][12] In 1861, a few months after the start of the American Civil War, Lilly enlisted in the Union Army and joined the 21st Indiana Infantry Regiment on July 24.

The 18th Indiana mustered into service at Camp Morton in Indianapolis on August 6, 1862, and spent a brief time drilling before it was sent into battle under Major General William Rosecrans in Kentucky and Tennessee.

Lilly's artillery unit was transferred to the Lightning Brigade, a mounted infantry under the command of Colonel, later General, John T. Wilder on December 16, 1862.

In September 1864, at the Battle of Sulphur Creek Trestle in Alabama, he was captured by Confederate troops under the command of Major General Nathan B. Forrest and held in a prisoner-of-war camp at Enterprise, Mississippi until his release in a prisoner exchange in January 1865.

[7][14][15] Lilly later obtained a large atlas, and marked the path of his movements during the Civil War and the location of battles and skirmishes in which he participated.

During his term, he helped organize a reunion and large parade in Indianapolis that brought together tens of thousands of Union Army veterans, including from the Lilly Battery.

In 1869, he began working for Patterson, Moore and Talbott, another medicinal wholesale company, before he moved to Illinois to establish a new business.

[3][19] Eli and Maria's only child, a daughter named Eleanor, was born on January 25, 1871, and died of diphtheria in 1884 at the age of thirteen.

Although the business in Illinois was profitable and allowed Lilly to save money, he was more interested in medicinal manufacturing than running a pharmacy.

[4][11] On May 10, 1876, Lilly opened his own laboratory in a rented two-story building at 15 West Pearl Street that has since been demolished, and began to manufacture drugs.

One of the first medicines he began to produce was quinine, a drug used to treat malaria,[23] that resulted in a "ten fold" increase in sales.

[22][25] By the late 1880s, Lilly had become one of the Indianapolis area's leading businessmen, with a company of more than one hundred employees and $200,000 ($5,760,741 in 2020 chained dollars) in annual sales.

In 1881, he purchased a complex of buildings at McCarty and Alabama Streets, south of downtown Indianapolis, and moved the company to its new headquarters.

[22][26] Believing that it would be an advantage for his son to gain a greater technical knowledge, Lilly sent Josiah to the Philadelphia College of Pharmacy in 1880.

[31] In 1879, with a group of 25 other businessmen, Lilly had begun sponsoring the Charity Organization Society, and soon became the primary patron of its Indiana chapter.

The Commercial Club members also helped fund the creation of parks, monuments, and memorials, as well as successfully attracted investment from other businessmen and organizations to expand Indianapolis's growing industries.

[34] During the Panic of 1893, Lilly created a commission to help provide food and shelter to the poor people who were adversely affected.

[35] Lilly's friends often urged him to seek public office, and they attempted to nominate him to run for Governor of Indiana as a Republican in 1896, but he refused.

Eli Lilly and Company played an important role in delivering medicine to the victims of the devastating 1906 San Francisco earthquake.

Innovation continued at the company after it was made a publicly traded corporation in 1952; it developed Humulin, Merthiolate, Prozac, and many other medicines.

[44] During his lifetime, Lilly had advocated for federal regulation on medicines; his son, Josiah, continued that advocacy following his father's death.