Jožef Stefan Institute recently commissioned a high brightness H− ion beam injection system for its existing tandem accelerator facility. Custom developed by High Voltage Engineering Europa, the multicusp ion source has been tuned to deliver at the entrance of the Tandetron™ accelerator H− ion beams with a measured brightness of 17.1Am−2rad−2eV−1at 170μA, equivalent to an energy normalized beam emittance of 0.767πmmmradMeV1/2. Upgrading the accelerator facility with the new injection system provides two main advantages. First, the high brightness of the new ion source enables the reduction of object slit aperture and the reduction of acceptance angle at the nuclear microprobe, resulting in a reduced beam size at selected beam intensity, which significantly improves the probe resolution for micro-PIXE applications. Secondly, the upgrade strongly enhances the accelerator up-time since H and He beams are produced by independent ion sources, introducing a constant availability of 3He beam for fusion-related research with NRA. The ion beam particle losses and ion beam emittance growth imply that the aforementioned beam brightness is reduced by transport through the ion optical system. To obtain quantitative information on the available brightness at the high-energy side of the accelerator, the proton beam brightness is determined in the nuclear microprobe beamline. Based on the experience obtained during the first months of operation for micro-PIXE applications, further necessary steps are indicated to obtain optimal coupling of the new ion source with the accelerator to increase the normalized high-energy proton beam brightness at the JSI microprobe, currently at 14Am−2rad−2eV−1, with the output current at 18% of its available maximum.