X-ray powder diffraction (XRPD)-based quantitative phase analysis is a common technique for studying the hydration of cementitious systems. Hydrated cements often comprise several amorphous or nanocrystalline phases. This paper presents a protocol for the quantification of amorphous siliceous fly ash in hydrated cement using XRPD based on the Rietveld PONKCS (partial or no known crystal structure) method. The protocol is validated by comparison against independent measurements, such as Ca(OH)(2) content by thermogravimetry and isothermal calorimetry to evaluate the fly ash degree of reaction. A sensitivity analysis of the protocol was carried out to test the robustness of the results with regard to sample preparation, data collection strategies and refinement model parameters. The key sensitive aspects of the protocol are (i) the preservation and preparation of the hydrated cement sample for XRPD measurement, (ii) the selection of a 2g theta angular range for the Rietveld analysis that avoids low-angle scattering interferences, and (iii) the use of the peak profile to account for the contribution of other amorphous phases such as the diffraction pattern of nanocrystalline calcium silicate hydrate (C-S-H). The results show good accuracy in terms of quantification if the initial fly ash content is more than 10 wt%. Example TOPAS fly ash and C-S-H codes, as well as the raw XRPD data set, are provided.