A novel modular end-station has been developed for use with focused MeV ion beams. It supports analysis of micro-samples using simultaneously several ion beam analysis (IBA) techniques, including wavelength dispersive (WD) and energy dispersive (ED) Particle Induced X-ray Emission (PIXE) spectrometry, Elastic Backscattering Spectrometry (EBS and RBS) and Nuclear Reaction Analysis (NRA). The end-station enables quantitative elemental analysis, including the creation of two-dimensional elemental maps based on the ED-PIXE and EBS/RBS/NRA measurements. The in-house developed wavelength dispersive X-ray (WDX) spectrometer can measure high energy resolution spectra on selected sample micro-regions. In this work the description of the modular end-station is presented, highlighting the features of the WDX spectrometer: i) in the complementary analysis of complex ED X-ray spectra with many overlapping peaks measured simultaneously and ii) in chemical speciation studies. An example is presented to demonstrate the capabilities of the modular system for simultaneous analytical measurements of selected heterogeneous micro-samples.