On March 21, 1944, the incoming Germans arrested the leader of the community. Oszkar Frischmann, businessman, was appointed to look after matters within the ghetto. At the end of April, he was ordered to submit the names of the Jews to the authorities. The ghettoization reached the district of Mosonmagyaróvár on May 10 and 297 names of Jews were forwarded to the police of Györ. The Moson ghetto was established May 15-17 in the Osztermayer and Mosonvar streets, located near the synagogue.

According to the Györi Nemzeti Hirlap newspaper, on May 23, 966 additional Jews from three districts of the county were brought in to the Mosonmagyaróvár ghetto and they had to bear the financial burden of the transportation.

Little information is available about the interior life of the ghetto. On May 26, Janos Sattler, the mayor of Mosonmagyaróvár, asked the authorities in vain to supply the ghetto inhabitants with the most necessary items, food, wood and clothing. In his request letter he wrote: "The Jewish families cannot cook, cannot wash their clothes and there is a public health danger. Most people have no change of clothing." On June 4, news was received that one man from Ménföcsanak committed suicide. On the morning of June 6, the ghetto inhabitants of Mosonmagyaróvár were transported by train to the ghetto in Györ.

In Györ ghetto four labor camps, with different levels of work, were operating. The camp kitchen was using equipment which the displaced Jews of Rajka and Mosonszentjanos had left behind. They performed heavy physical labor in various local factories. In June 1944 several thousand Jews from the Györ ghetto, including those from Mosonmagyaróvár were transported to Auschwitz.

Starting in November 1944 the German started to march on foot thousands of Budapest Jews to the Austrian border and Mosonmagyaróvár became one of the overnight and feeding stations. They were very badly treated by the German guards and Hungarian gendarmes, many died or were killed, some in Mosonmagyaróvár. In the cemetery there is a monument for these victims.

A memorial for Jews from Budapest who where force-marched in November 1944 to the Austrian border to work on fortifications. It is unclear how many were killed in Mosonmagyarovar.