Helmy was conscripted for service in the local health corps, and used his position to provide medical excuses for foreign laborers to leave Germany and for Germans to avoid military service. He worked to secretly treat Jewish citizens and help hide them from persecution., including Anna Boris, a patient whom he successfully hid from the authorities until the end of the war. At one point, when Helmy's activities were close to discovery, he and Boros concocted a scheme to make it appear that she had duped him - a ruse that played on the Gestapo's belief that Helmy, as a "Hamite" was innately unintelligent.
Helmy died in 1982 in Berlin. He was subsequently named as one of the Righteous Among the Nations, the roll of honor for non-Jews who risked their lives during the Holocaust to protect Jews from the Nazis.