Emilio Aguinaldo, who led the Philippine war against America, wrote retrospectively in 1957 that McKinley's instructions to the commission would "prove one of the most important documents in the history of international relations.

[5] Between September 1900 and August 1902, it issued 499 laws, established a judicial system, including a Supreme Court, drew up a legal code, and organized a civil service.

The instruction also gave the Commission the power to appoint officers under the judicial, educational, and civil service systems and in the municipal and departmental governments.

[5] Mindful of pacification efforts following the Philippine–American War and as an early step towards to preparing the Philippines for eventual self-governance, in 1903 the commission passed the Pensionado Act establishing a scholarship program for Filipinos to attend school in the United States and allocating $72,000 for the purpose (equivalent to $2,441,600 in 2023).

[9] In a statement published on September 1, 1900, the commissioners announced the holding of public meetings every Wednesday and Friday to allow interested parties to comment and make suggestions on proposed legislative matters.

[10] William Forbes, later Governor General of the Philippines, wrote that he could not remember any instance where a commissioner protested because he could not understand an issue on linguistic grounds.

[11] A few months before the inauguration of Taft as governor-general, Senator John Spooner filed a bill giving unprecedented powers to the executive branch in the development of colonial policy in the Philippines.

[16] Emilio Aguinaldo wrote in 1957 that the Spooner Amendment had laid the basis of a far-sighted and enlightened economic policy in the Philippines.

The act provided that future appointments of the civil governor, vice-governor, members the Philippine Commission, and heads of Executive Departments shall be made by the President, by and with the advice and consent of the Senate.

[7][18][19] The Taft Commission promulgated a total of 157 laws between September 1900 and July 4, 1901, when Taft became Civil Governor, classified as follows:[20] Following the advice of McKinley to start at the bottom and gradually move upward, over seventy percent of the laws dealt with local government and the bureaucracy; with more than half of these being acts extending the provision of the Provincial Government Act to the different provinces.

[21] The Commission created and reorganized government offices, including the following:[22][23] President McKinley had declared in his message to Congress in December 1899 that Philippine reconstruction should proceed by building up from the bottom.

[30] McKinley's instruction to the Commission stressed that the establishment of civilian government should start from the smallest unit of political organization and gradually move towards Manila.

[36] Commissioner Bernard Moses, who had been an educator at the University of California, worked with Captain Albert Todd and Dr. Fred Atkinson to draft Act No.

The Thomasites had a difficult time convincing their students to give more importance to activities that developed critical thinking than to those which simply required rote memorization, or that coming an hour late or being absent to attend a town fiesta was a big shortcoming.

[43] Another problem encountered was difficulty in promoting equality among the students, as children of wealthy families thought they were entitled to special privileges.

[45] The instructions of President McKinley to the commission stipulated that it was their duty to make a thorough investigation into the titles of large tracts of land held or claimed by individuals or by religious orders.

[49] The Philippine Organic Act, enacted in July 1902, authorized the Insular Government to purchase the friar lands, empowering it to issue bonds for the purpose.

Taft commissioned a survey to determine their market value, and a purchase price of $7,239,784.66 was paid in December 1903 by the Insular Government.