At the young age of 24, Kellogg became the medical superintendent of the Western Health Reform Institute, later renamed the Battle Creek Sanitarium. He immediately began implementing his ideas on diet, exercise, and hygiene.

Under Kellogg's leadership, the Sanitarium expanded significantly, becoming a world-renowned health resort. He introduced innovative treatments such as hydrotherapy, phototherapy, and mechanical exercise. He also developed and promoted a vegetarian diet, emphasizing whole grains and fiber.

While experimenting with ways to improve the palatability of grains, Kellogg and his brother Will Keith Kellogg accidentally discovered the process of creating flaked cereal. This marked the beginning of the ready-to-eat cereal industry.

The Battle Creek Sanitarium reached the height of its popularity, attracting thousands of patients each year, including prominent figures from around the world. Kellogg became a celebrity doctor and health guru.

A devastating fire destroyed the main building of the Battle Creek Sanitarium. This was a major setback, but Kellogg quickly rallied support and oversaw the construction of a larger and more modern facility.

Despite the fire, Kellogg continued to operate the Sanitarium and promote his health principles. He wrote extensively on topics such as diet, exercise, and sexuality, and lectured widely. While the sanitarium was rebuilt, it never fully regained it's place of popularity.

The Sanitarium gradually declined in popularity as medical practices evolved and the novelty of Kellogg's approach wore off. Financial difficulties also contributed to its decline.

John Harvey Kellogg died at the age of 91 in Battle Creek, Michigan. The Sanitarium continued to operate under different management for a few years before eventually closing.