In 1894 Luna moved back to the Philippines and traveled to Japan in 1896,

returning during the Philippine Revolution of the Cry of Balintawak.

Unfortunately, on September 16, 1896, he and his brother Antonio Luna
were arrested by Spanish authorities for being involved with the Katipunan
rebel army.[7] Despite his imprisonment, Luna was still able to produce a
work of art which he gave to a visiting priest. He was pardoned by the
Spanish courts on May 27, 1897 and was released from prison and he
traveled back to Spain in July.[8]:394 He returned to Manila in November
1898.[8]:394 In 1898, he was appointed by the executive board of the
Philippine revolutionary government as a member of the Paris delegation
which was working for the diplomatic recognition of the Repblica Filipina
(Philippine Republic). In 1899, upon the signing of the Treaty of Paris
(1898),[9] Luna was named a member of the delegation to Washington, D.C.
to press for the recognition of the Philippine government.
He traveled back to the Philippines in December 1899 upon hearing of the
murder of his brother Antonio by the Kawit Battalion in Cabanatuan. He
traveled to Hong Kong and died there on December 7, 1899 from a heart
attack. His remains were buried in Hong Kong and in 1920 were exhumed
and kept in Andrs Luna's house, to be later transferred to a niche at the
Crypt of the San Agustin Church in the Philippines. Five years later, Juan
would be reinstated as a world-renowned artist and Peuple et Rois, his last
major work, was acclaimed the best entry to the Saint Louis World's Fair in
the United States.[10] Unfortunately some of his paintings were destroyed by
fire in World War II.