Alkaline carbonatite complexes are formed by magmatic, hydrothermal, and weathering geological events, which modify the minerals present in the rocks, resulting in ores with varied metallurgical behavior. To better spatially distinguish ores with distinct plant responses, creating a 3D geometallurgical block model was necessary. To establish the clusters, four different algorithms were tested: K-Means, Hierarchical Agglomerative Clustering, dual-space clustering (DSC), and clustering by autocorrelation statistics. The chosen method was DSC, which can consider the multivariate and spatial aspects of data simultaneously. To better understand each cluster’s mineralogy, an XRD analysis was conducted, shedding light on why each cluster performs differently in the plant: cluster 0 contains high magnetite content, explaining its strong magnetic yield; cluster 3 has low pyrochlore, resulting in reduced flotation yield; cluster 2 shows high pyrochlore and low gangue minerals, leading to the best overall performance; cluster 1 contains significant quartz and monazite, indicating relevance for rare earth elements. A hierarchical indicator kriging workflow incorporating a stochastic partial differential equation (SPDE) trend model was applied to spatially map these domains. This improved the deposit’s circular geometry reproduction and better represented the lithological distribution. The elaborated model allowed the identification of four geometallurgical zones with distinct mineralogical profiles and processing behaviors, leading to a more robust model for operational decision-making.