In this paper, zonation patterns of trace elements in fluorapatite are discussed that were visualized using four analytical techniques, namely back-scattered electrons (BSE) and cathodoluminescence (CL) imaging, electron probe micro-analysis (EPMA), and micro-proton-induced X-ray/ gamma ray emission (μPIXE/μPIGE) mapping. Each method demonstrates the in-grain compositional variations in a slightly different way. Both BSE and CL provide qualitative data, and the internal textures are displayed in most detail. Additionally, CL points to specific elements enriched in certain growth zones. Qualitative EPMA maps show detailed zonation patterns for specific elements (with high spatial resolution), which are in general correspondence with the patterns observed in BSE and CL images. The μPIXE/μPIGE maps are fully quantitative and the detection limits are relatively low compared to EPMA mapping. In present spot measurements μPIXE demonstrates lower detection limits than EPMA, however, the latter could be considerably improved by extending the acquisition times. There is no significant overlap of REE (rare earth elements) peaks in the acquired μPIXE energy spectra, however, when multiple REEs are present with sufficiently high concentrations, peak deconvolution may pose some difficulties. Spatial resolution of μPIXE/μPIGE images is not sufficiently high to reflect minor textural features, which also result from the greater interaction depth of the proton beam. However, major growth zones are distinguishable. Even though each method has their advantages and limitations, when applied together, they provide an almost complete characterization of compositional variability in trace-element-bearing minerals.