From 1919, Lohse was first an associate at the Schleswig-Holstein Farmers' Association, and then as of 1920 General Secretary of the Schleswig-Holsteinische Bauern- und Landarbeiterdemokratie. In 1923 he joined the Nazi Party and became on 27 March 1925 the NSDAP Gauleiter for Schleswig-Holstein. In 1924, as a member of the Völkisch-Sozialer Block list, he became the only Nazi to be elected to the city representative college (Stadtverordnetenkollegium) of Altona/Elbe. During this time, he led various nationally-oriented farming associations in northern Germany, such as the Landvolkbewegung ("Rural People's Movement"), into the Nazi Party. Between 1928 and 1929, Lohse also temporarily administered the Nazi Gau of Hamburg.
On 17 July 1941, after the German occupation of Baltic states from the Soviet Union, Lohse was appointed the "Reichskommissar for the Ostland". Lohse retained his functions in Schleswig-Holstein and shuttled between his two seats of Riga and Kiel. After taking office, Lohse filled many important posts with likeminded old friends from Schleswig-Holstein. He held this function until he left, or rather fled, the Reichskommissariat Ostland in the autumn of 1944. In Schleswig-Holstein, during the time when Nazi Germany was losing power, he still exercised absolute rule as Reich Defence Commissar.
On 6 May 1945, owing to British demands, Lohse was unseated as High President of Schleswig-Holstein by Reich President Karl Dönitz. Shortly thereafter, he was seized by the British Army. Lohse was sentenced in 1948 to 10 years in prison, but was released in 1951 due to illness. Two inquiries were launched by prosecutors against him; the grant of a High-Presidential pension which Lohse was fighting for was withdrawn under pressure from the Schleswig-Holstein Landtag. Lohse spent his twilight years in Mühlenbarbek.