Nephrolithiasis, or kidney stone formation, is a widespread global health concern. This study examines the effects of polyphenolic extracts, along with their anthocyanin and non-anthocyanin fractions, from sumac fruit, pomegranate peel, almond leaves, falsa fruit, and banana bract on the crystallization of calcium oxalate (CaC2O4.nH2O) and brushite (CaHPO4 2H2O) in vitro. The extracts were prepared through maceration in aqueous methanol and further fractionated into anthocyanin and non-anthocyanin fractions using solid-phase extraction. For calcium oxalate crystallization, nucleation and aggregation were monitored using a spectrophotometer in the presence and absence of these extracts and fractions. For brushite crystallization, the single diffusion gel growth method was employed. All extracts inhibited the crystallization of both calcium oxalate and brushite in a dose-dependent manner, significantly reducing crystal number, size, and altering crystal morphology. Non-anthocyanin fractions demonstrated a stronger inhibitory effect than anthocyanin fractions. Molecular docking studies further revealed that compounds in these fractions exhibited strong binding affinity with proteins involved in the adhesion and aggregation of calcium oxalate crystals to renal cells, supporting their anti-lithogenic properties. These findings suggest that these natural polyphenolic sources hold promise as potential inhibitors of kidney stone formation.