Afterward, he shifted his focus to business endeavors, particularly in coconut farming and processing, cattle raising, and maritime shipping lines.

[2] Shortly thereafter in September 1890, Worcester and fellow zoologist Frank Swift Bourns returned to the Philippines on a two-year zoological expedition funded by Louis F. Menage, a wealthy Minneapolis businessman who was the major benefactor of the Minnesota Academy of Natural Sciences.

[2][8] Worcester had a keen interest in public health, but his response to a major 1902–04 outbreak of cholera in Manila and other Philippine cities was highly criticized.

[2] In response, the Insular Department of Interior, primarily under the authorship of Worcester, published a history of these cholera outbreaks with an account of the agency's attempts to control them.

[10] On October 30, 1908, El Renacimiento, a daily newspaper in Spanish, published an editorial written by Fidel A. Reyes (1878–1967), its city editor, titled "Aves de Rapiña" ("Birds of Prey"), which denounced an American official for using his office to exploit the resources of the country for his personal gains.

[12] Worcester was alleged to have used his anthropological research to seek out gold in Benguet and exploit untapped natural resources in Mindoro and Mindanao.

'"[13] Although the editorial did not mention names, Worcester felt that he was the public official referred to and filed a libel case against Reyes, as well as editor Teodoro Kalaw and publisher Martin Ocampo, among several others.

[2] Despite Worcester's resignation from public office, Worcester remained as a focus of Filipino animosity largely for his unfavorable depiction of Filipinos in The Philippine Islands and Their People and his high-profile public opposition of the 1912 and 1914 "Jones Bills" that were eventually passed by the United States Congress as the Jones Act of 1916 that restructured the Insular Government and began a process for full Philippine independence.

[17] At issue according to Kalaw was that Worcester had published in 1914 The Philippines Past and Present in which he again used the power of his photography to depict "primitive" Filipinos juxtaposed with photos of the modern infrastructure brought by the Americans, particularly during his own tenure as Secretary of the Interior.

But the protests against Worcester subsided in late 1916 once the Jones Act was passed into law and the coconut oil exports were beginning to substantially fuel the local economy in Cebu.

Worcester also had close relations with Dr. William Hutchins Boynton (1881–1959) the chief veterinary pathologist with the Philippine Bureau of Agriculture who by 1918 had developed an early vaccine for rinderpest, a devastating disease of cattle.