Quantification of halloysite and kaolinite in clay deposits from X-ray diffraction (XRD) commonly requires extensive sample preparation to differentiate the two phyllosilicates. When assessing hundreds of samples for mineral resource estimations, XRD analyses may become unfeasible due to time and expense. Fourier transform infrared (FTIR) analysis is a fast and cost-effective method to discriminate between kaolinite and halloysite; however, few efforts have been made to use this technique for quantified analysis of these minerals. In this study, we trained machine- and deep-learning models on XRD data to predict the abundance of kaolinite and halloysite from FTIR, chemical composition, and brightness data. The case study is from the Cloud Nine kaolinite–halloysite deposit, Noombenberry Project, Western Australia. The residual clay deposit is hosted in the saprolitic and transition zone of the weathering profile above the basement granite on the southwestern portion of the Archean Yilgarn Craton. Compared with XRD quantification, the predicted models have an R2 of 0.97 for kaolinite and 0.96 for halloysite, demonstrating an excellent fit. Based on these results, we demonstrate that our methodology provides a cost-effective alternative to XRD to quantify kaolinite and halloysite abundances.