Kidney stones consisting predominantly of whewellite (calcium oxalate monohydrate, COM) are often found attached to hydroxylapatite (HA) plaques that form in the soft tissue of kidneys, cause lesions and become exposed to urine. Although the processes of stone formation are not entirely known, it is an established view that so-called Randall’s plaques serve as substrates for COM crystal nucleation and growth from correspondingly supersaturated urine. However, the results presented here suggest an additional mineral replacement process is involved. In an experimental approach, HA was reacted in 0.25 mM, 0.5 mM and 1.0 mM oxalate solutions with pH ranging from 4.5 to 7.5, simulating normal to harsh conditions encountered in urine. Extremely acidic solutions induce dissolution of HA crystals coupled with re-precipitation of the released Ca2+ ions as COM on the HA surface. When, instead, bone was used as a substrate, being more similar to the pathological plaque (aggregated HA nanocrystals within an organic matrix), the HA-COM mineral-replacement reaction is induced even under much milder fluid conditions, commonly found in urine. Hence, a process of COM partly replacing and encrusting Randall’s plaque may take place in the urinary tract of idiopathic stone formers, representing a potential starting event for nephrolithiasis.