In September 1913, the United Mine Workers of America declared a strike against the Colorado Fuel and Iron (CF&I) company in what would become the Colorado Coalfield War. Junior owned a controlling interest in CF&I (40% of its stock) and sat on the board as an absentee director. In April 1914, after a long period of industrial unrest, the Ludlow Massacre occurred at a tent camp occupied by striking miners. At least 20 men, women, and children died in the slaughter. This was followed by nine days of violence between miners and the Colorado National Guard. Although he did not order the attack that began this unrest, there are accounts to suggest Junior was mostly to blame for the violence, with the awful working conditions, death ratio, and no paid dead work which included securing unstable ceilings, workers were forced into working in unsafe conditions just to make ends meet. In January 1915, Junior was called to testify before the Commission on Industrial Relations. Many critics blamed Rockefeller for ordering the massacre. Margaret Sanger wrote an attack piece in her magazine The Woman Rebel, declaring, "But remember Ludlow! Remember the men and women and children who were sacrificed in order that John D. Rockefeller Jr., might continue his noble career of charity and philanthropy as a supporter of the Christian faith."
He established the Bureau of Social Hygiene in 1913, a major initiative that investigated such social issues as prostitution and venereal disease, as well as studies in police administration and support for birth control clinics and research. In 1924, at the instigation of his wife, he provided crucial funding for Margaret Sanger (who ironically had previously been an opponent of his because of his mistreatment of workers) in her work on birth control and involvement in population issues. He donated five thousand dollars to her American Birth Control League in 1924 and a second time in 1925.