The last two transport trains to leave Sereď during this time carried patients from the local Jewish hospital, as well as physically and mentally disabled people from various medical institutes.

In this later phase, Sereď was guarded by local police, who opened the gates and let the remaining Jews escape after the beginning of the Slovak National Uprising.

In September 1944, Sereď was transformed into a concentration camp with an SS guard under the command of Bratislava German Franz Knollmayer.

The new contingent of SS soldiers proceeded to commit major atrocities against the prisoners, including torture, rape (though this was frowned on as a violation of racial hygiene laws), and murder.

In separate parts of the camp were imprisoned soldiers of the Slovak insurrectionist army, partisans, and people accused of supporting the uprising.