His trip to Brazil was further delayed for two years by the onset of World War I, political unrest in Haiti, and a plague epidemic in Cuba.

After serious disagreements with (and pressure from) the Swedish Royal Academy of Science in Stockholm, Ekman returned to the island of Hispaniola in 1924 and is credited with having discovered hundreds of new species during his 7-year stay there.

[1] He collected in southwestern Haiti's Massif de la Hotte in and around present-day Pic Macaya National Park from December 1926 to January 1927 with Henry D. Barker, and again in September 1928.

[2] He collected primarily in Haiti from 1924 to 1928 and in the Dominican Republic from 1928 until his death in Santiago de los Caballeros on January 15, 1931, at the age of 46.

Ekman was interred in Santiago de los Caballeros, where a plaque was erected in his honor by the Dominican government and the American Society of Plant Taxonomists on October 14, 1950.

Ekman's published account and unpublished field notes provide detailed descriptions of the flora of the Selle and Hotte massifs as they existed in the 1920s.

Ekman also collected birds, mammals and reptiles, of which several species bear his name, e.g. the Hispaniolan nightjar (Antrostomus ekmani).