Szczebrzeszyn was occupied by the Germans on Rosh Hashana (September 13th, 1939). Except for a two week period when the Germans withdrew in favour of the Red Army, their return brought with it further daily acts of violence and assault, including shearing the beards and sidelocks of religious Jews. Every day too Jews were abducted for slave labour. Males aged from 15 to 60 were taken to work in military encampments in Zamosc and to build an airfield near Budaczew. In December the Jews were ejected from their houses and crammed into one section of the town, which was in effect an open ghetto.
By April 1942 there were more than 3,000 Jews in the ghetto, both local and refugees. When rumours reached S of deportation from the Lublin district to the death camps, many Jews sought refuge in nearby villages or tried to find hiding-places and bunkers in the ghetto itself. Acts of murder and deportation to the camps began in Szczebrzeszyn in May 1942, and continued throughout the summer. On May 8th the Gestapo arrested two men and two women in the middle of the night, took them to nearby Zwierzyniec and there killed them. In the morning Gestapo personnel arrived from Zamosc, rounding up some 2,000 Jews in the town square and opening fire on them. About a hundred Jews were killed and many others wounded. The Germans started sending hundreds of Jews at a time from the ghetto to the extermination camps at Belzec, and in the direction of Bilgoraj while murdering others in a field outside the town. On August 8th some 400 Jews were taken to the railway station, crammed into goods wagons and sent to Belzec. Another 200 elderly Jews were taken that same day outside the town and there shot to death. A few days later the Germans sent some 700 Jews to the labour camp near Chelm, where they too were killed.
The days October 21st-24th marked the end of the community of Szczebrzeszyn, when the last survivors were sent to extermination at Belzec.
During these arrests and deportations many tried to escape to the woods, but the number who survived was small. Many were caught on the way and shot; others were handed over to the Germans by Polish collaborators, or shot by peasants in whose houses they sought refuge. However, there were a few Poles who saved Jews at the risk of their own lives. The hostile attitude of the local Polish population made the flight to the woods difficult, but despite this, hundreds of Jews succeeded in reaching them and there organised partisan activity. Most of these though were killed and only a small remnant lived to experience liberation.