In 1888, the Recoletos erected a wooden Santa Cruz outside the San Agustin Church, the same cross which still stands today outside the present San Agustin Cathedral.

In late August of 1896, the Katipunan revolution against Spain broke out in Luzon. Exactly a month after, or September 29, 1896, a group of Filipinos from Luzon deported to the Spanish fort in Iligan for military discipline, mutinied against the Spanish Officers and soldiers after receiving instructions from the Katipunan in Manila. They were able to raid the Spanish armonry, and with ammunitions in hand, proceeded to Cagayan to attack the town. On the way to Cagayan, they ransacked all the convents and homes of Spanish peninsulars along the way. From Cagayan, they proceeded to Bukidnon where a band of natives joined the resistance. They then attacked Balingasag, and raided the outpost of Gingoog on January 1897. By that time, news of Rizal's execution had reached Cagayan and Misamis, and this further angered the townfolks, fanning the flames of the local Katipuneros. It took a Spanish gunboat, recalled from the Tercio Distrito de Surigao, to subdue the resistance. This was the only known Katipunan revolt in the whole of Mindanao.

On December 10, 1898, the Treaty of Peace between the warring United States and Spain signed in Paris. Immediately, the reigning Spanish governor of Misamis resigned and relinquish his authority to the Filipino local officials of Cagayan town and Misamis province who were elected according to the provisions of General Emilio Aguinaldo decreed earlier in Malolos on June 1898. The first Filipino governor of Misamis was Jose Roa y Casas and the first municipal mayor of Cagayan was Toribio Chaves. The revolutionary junta already ruled Cagayan by late December 1898. On January 10, 1899, the town of Cagayan celebrated the First Philippine Republic of Aguinaldo with a two-day celebration known as the Fiesta Nacional with a parade, music, speeches, and the boom of cannonades outside the Casa Real. It was the first time that the Aguinaldo Republic was proclaimed in Mindanao and the first time that the new Filipino tricolor flag was raised in Mindanao. This local government ruled uninterrupted until the invasion of the Americans on March 1900.

The Americans invaded Cagayan by bombarding the Filipino flag that fluttered at Macabalan wharf on March 31, 1900. By the time, Cagayan revolutionaries were already massed and prepared to fight against the new colonizers. Led by General Nicolas Capistrano, the town of Cagayan de Misamis fought gallantly in the Philippine-American War and was one of only two such theaters in that war in the entire Mindanao. The Cagayan resistance fighters first fought in the Battle of Cagayan on April 7, 1900 in the center of town. This was followed by the Battle of Agusan Hill that was led by Captain Vicente Roa y Racines who was martyred with his men by the Americans. The US forces only lost to the Cagayan fighters in the Battle of Makahambus Hill under Colonel Apolinar Velez on June 4, 1900 where a great number of American soldiers perished. It was the first victorious battle of the Filipinos in the entire duration of the Philippine-American War in the whole country.