Winkler re-enlisted in the Austrian army at the outbreak of World War I in 1914, and was decorated twice for bravery before being wounded in November 1915. During a lengthy recovery, he worked for the War Economy committee; his talents were recognized and he was appointed Secretary of State for Military Affairs at the end of the war in 1918 and he was a delegate to the Versailles Peace Conference. That year, he also married a Jewish woman named Clara Deutch. He joined the Austrian Central Statistics Office in 1920, and was promoted to director of its department of population statistics in 1925. Concurrently, he became a "Privat-Dozent" (assistant professor) at the University of Vienna in 1921 and an "Ausserordentlicher Professor" in 1929. He founded an institute for the study of minority populations, which published a constant stream of progressive and influential papers that made him unpopular with colleagues in his government job. Despite his lack of formal education, he was elected a member of the International Statistical Institute in 1926 where he actively promoted applied and precise mathematical formulations in contrast to the wordy generalizations that he had criticized 20 years earlier. As both the husband of a Jew and an outspoken critic of the unfair treatment of European minorities, Winkler was promptly fired from both his government and academic positions following the 1938 Nazi annexation of Austria. Despite severe persecution from the Nazi party, he wrote the textbook "Basic Course in Demography" during the occupation.