Pathological calcification is a wide-spread phenomenon in the human body, in which calcium minerals form in soft tissues and are found in both healthy and diseased tissues. One example are microcalcifications (MCs), which are primarily biological apatite and occur in cancerous and benign breast pathologies. MCs are key mammographic indicators, however, little is known about their materials properties and associated organic matrix, or their correlation to breast cancer prognosis. Outside the clinic, numerous microcalcification compositional metrics (e.g., carbonate and metal content) are linked to malignancy, yet microcalcification formation is dependent on microenvironmental conditions, which are notoriously heterogeneous in breast cancer. We have interrogated multiscale heterogeneity in calcifications from over 20 breast cancer patients. Employing an omics-inspired approach, for each microcalcification we define a “biomineralogical signature” combining metrics derived from Raman microscopy and energy dispersive spectroscopy. We observe that 1) calcifications cluster into physiologically relevant groups reflecting tissue type and local malignancy; 2) carbonate content exhibits substantial intratumor heterogeneity; 3) trace metals including zinc, iron, and aluminum, are enhanced in malignant-localized calcifications; 4) the lipid-to-protein ratio within calcifications is lower in patients with poorer prognosis, suggesting that expanding diagnostic metrics to include “mineral-entrapped” organic material may hold prognostic promise.  This multimodal methodology lays the groundwork for establishing MC heterogeneity in the context of breast cancer biology, and has the potential to be applied to other pathological minerals, as well as in vitro models of mineralization.