In Poland, he led a 70-man SS unit that, in addition to guard duties, trained the "Volksdeutscher Selbstschutz" in Piotrków Trybunalski, as well as the Opoczno and Rawa districts.

[1] Initially, Michalsen was assigned to the staff of SS-Oberführer Fritz Katzmann, the SS and Police Leader (SSPF) in the Radom District of the General Government.

Beginning on 27 July, approximately 7,000 Jews per day were transported by train for alleged "resettlement" to the east, however, the true destination of the deportations was the Treblinka extermination camp.

[5] In addition to the operation in Warsaw, Michalsen, together with others in Lublin cadre, played a leading role in the evacuation of the ghettos in Otwock, Wołomin, Piaski, Międzyrzec Podlaski and Włodawa.

During the final destruction of the Warsaw Ghetto in April and May 1943, Michalsen organized the relocation to a site in Lublin of the Többens and Schultz factories that employed thousands of forced laborers.

"[6] Following the armistice between Fascist Italy and the Allies, now SS-Gruppenführer Globočnik on 13 September 1943 was promoted to the newly created post of Higher SS and Police Leader (HSSPF) in the Operational Zone of the Adriatic Littoral, with headquarters in Trieste.

[8] Finally, on 27 October 1944, he was officially given the post of SS and Polizeigebietkommandeur (Police Area Commander) in Trieste,[9] which was the site of the Risiera di San Sabba, a concentration and transit camp where it is estimated that over 3,000 persons were killed.

After the end of the war in Europe, Michalsen was captured on 31 May 1945 together with Globočnik, Höfle and Lerch on an alpine pasture (Möslacher Alm) near the Weissensee Lake in Carinthia.