Chruściel's regiment was secretly mobilised between 23 and 27 March 1939, and moved to the village of Szczerców where it formed a defensive line at the Widawka River. After the outbreak of the Polish Defensive War of 1939 it entered combat on 2 September. As part of the "Piotrków Operational Group" of the Łódź Army, Chruściel's unit retreated towards the Modlin Fortress and took part in its defence until the capitulation of the Polish units in the area. Interned in the POW camp in Działdowo, he was released in late October, already after the end of hostilities. Fearing that his release from the prison camp was a mistake, Chruściel moved to Warsaw, where he settled under a variety of false names. In June 1940 he joined the Union of Armed Struggle (ZWZ) underground organization. Initially head of the 3rd division of its staff, responsible for training and tactics, since October of that year Chruściel held the post of deputy commander of the City of Warsaw ZWZ region.