As part of his missionary work, Boeynaems sailed to the Kingdom of Hawai‘i arriving in Honolulu on November 29, 1881, to become a pastor (in January 1882) to the fledgeling Catholic community of native Hawaiians on the island of Kaua‘i in the district encompassing Līhu‘e to Hanalei. He later ministered to those on Kaua‘i in the district encompassing Līhu‘e to Mana. During his first few years in Honolulu, Boeynaems was a witness to the 1893 overthrow of the Hawaiian monarchy, proclamation of the Republic of Hawai‘i and establishment of the United StatesTerritory of Hawai‘i. In 1895 he was transferred to Wailuku, Maui. In December, 1902, the Holy See appointed him Pro-Vicar. On April 8, 1903, he was appointed Vicar Apostolic and was subsequently consecrated titular Bishop of Zeugma in Syria by Archbishop Montgomery in Saint Mary's Cathedral in San Francisco on July 25, 1903. On April 11, 1915, Msgr. Boeynaems consecrated Saint Agnes-in-the-Palms at Kaka‘ako, a former Protestant church at the intersection of Kawaiahao and Kamani streets in Honolulu, to serve the growing population of Portuguese and native Hawaiians in the Kaka‘ako district. After his death, he was buried at the Honolulu Catholic Cemetery in downtown Honolulu near Thomas Square at the intersection of Ward Avenue and King Street.