External (in air) PIGE methodology has been optimized for rapid quantification of fluorine, sodium, and phosphorus in fluorapatite waste immobilization matrices for Molten Salt Reactor (MSR). The present methodology addresses the issue of distinguishing hydroxyapatite and fluorapatite phases through XRD patterns. Fluctuations in proton beam current have been monitored by prompt γ-ray from nitrogen (2312 keV) through ¹⁴N(p,p′γ)¹⁴N nuclear reaction and have successfully been applied as a new method of current normalization, for the first time, in external PIGE method with lower Compton background and negligible spectral interference. The proposed method was also compared with the earlier method of current normalization using 165 keV (¹⁸¹T(p,p′γ)¹⁸¹Ta) from the Tantalum window used for obtaining “in air” beam. For the fluctuation of beam current within 5–10 nA, nitrogen from air can be used as an effective current normalizer. Moreover, the uncertainty (within ±3%) was also improved in the present method of current normalization. Fluorine can be estimated from trace to major concentrations using 197 keV (¹⁹F(p,p′γ)¹⁹F) γ-ray with highest sensitivity as compared to other prompt γ-rays (110 keV and 1236 keV). The matrix effect in PIGE was also eliminated by diluting the sample in cellulose. The method was validated using the synthetic samples (Ca₁₀(PO₄)₆F₂, Na₂Eu₂Ca₆(PO₄)₆F₂, Na_1.5Eu_1.5Ca₇(PO₄)₆F₂, Na₁Eu₁Ca₈(PO₄)₆F₂, Na_0.5Eu_0.5Ca₉(PO₄)₆F₂, and Sr₁₀(PO₄)₆F₂). The results were found to be satisfactory and in good agreement with stoichiometric amounts. Elements such as Na, P, and Ca were determined in the fluorapatite samples using PIGE and EDXRF, respectively, as a part of chemical quality control. Moreover, in external PIGE, 1266 keV γ-ray (³¹P(p,p′γ)³¹P) provides more accurate P concentrations in the samples.