With the onset of World War II in 1939, the Special Education Institute was closed, and Grzegorzewska began working as a nurse in an army hospital run by the Polish Red Cross. Between 1939 and 1944, she taught at Special School No. 177 in Warsaw and participated in the clandestine educational system. Active in the Polish resistance movement, she distributed arms and pamphlets; joined Żegota, providing "meritorious" assistance to Jews; and took part in hiding Jews to save their lives. She served as a member of Ochota's health patrol during the Warsaw Uprising. During the uprising, her house was destroyed, and in it, unpublished manuscripts of two of her books, second volume of "Psychology of the Deaf" (), first volume published in 1930) and "Teacher's Personality" (). After Poland was liberated in 1945, Grzegorzewska reactivated the Special Education Institute, which had been destroyed during the conflict. Recognizing that 30% of the teachers had died in the war, she initiated programs to help train new teachers quickly. The Polish Teachers' Union was reestablished and she began research to evaluate existing educational programs, teachers' socio-economic status, and the role of schools in their communities, among other topics.