The measurement of near-infrared (NIR) cathodoluminescence (CL) with sufficient sensitivity to allow full spectral mapping has been investigated through the application of optimized grating spectrometers that allow the ultraviolet (UV), visible, and NIR CL spectra to be measured simultaneously. Two optical spectrometers have been integrated into an electron microprobe, allowing simultaneous collection of hyperspectral CL (UV-NIR), characteristic X-rays, and electron signals. Combined hyperspectral CL spectra collected from two natural apatite (Ca5[PO4]3[OH,F]) samples from Wilberforce (Ontario, Canada) and Durango (Mexico) were qualitatively analyzed to identify the emission centers and then deconvoluted pixel-by-pixel using least-squares fitting to produce a series of ion-resolved CL intensity maps. Preliminary investigation of apatite has shown strong NIR emissions associated primarily with the rare-earth element Nd. Details of growth and alteration were revealed in the NIR that were not discernable with electron-induced X-ray mapping. Intense emission centers from Nd3+ and Sm3+ were observed in the spectra from both apatites, along with minor emissions from other 3+ rare-earth elements. Quantitative electron probe microanalysis was performed on points within the mapped area of the Durango apatite to produce a calibration line relating cathodoluminescent intensity of the fitted peak centered at 1,073 nm (1.156 eV) to the Nd concentration.