The X-ray scanning microscope PtyNAMi at beamline P06 of PETRA III at DESY in Hamburg, Germany, is designed for high-spatial-resolution 3D imaging with high sensitivity. Besides optimizing the coherent ux density on the sample and the precision mechanics of the scanner, special care has been taken to reduce background signals on the detector. The optical path behind the sample is evacuated up until the sensor of a four-megapixel detector that is placed into the vacuum. In this way, parasitic scattering from air and windows close to the detector is avoided. The instrument has been commissioned and is in user operation. The main commissioning results of the low-background detector system are presented. A signal-to-noise model for small object details is derived that includes incoherent background scattering.