Phyllanthus niruri (Pn) is a plant that has been shown to interfere in the growth and aggregation of calcium oxalate (CaOx) crystals. In the present study we evaluated the effect of Pn on the preformed calculus induced by introduction of a CaOx seed into the bladder of male Wistar rats. Pn treatment (5 mg/rat/day) was initiated immediately or 30 days after CaOx seeding and thus in the presence of a preformed calculus. Animals were sacrificed 50 or 70 days after surgery. The resulting calculi were weighed and analyzed by X-ray diffraction, stereomicroscopy and scanning electronic microscopy. Precocious Pn treatment reduced the number (75%, P < 0.05) and the weight (65%, P < 0.05) of calculi that frequently exhibited a matrix-like material on its surface, compared to the untreated CaOx group. In contrast, Pn treatment in the presence of a preformed calculus did not prevent further calculus growth; rather, it caused an impressive modification in its appearance and texture. Calculi from Pn-treated animals had a smoother, homogeneous surface compared to the spicule shape of calculi found in the untreated CaOx group. XRD analysis revealed the precipitation of struvite crystals over the CaOx seed and Pn did not change the crystalline composition of the calculi. This suggests that Pn interfered with the arrangement of the precipitating crystals, probably by modifying the crystal–crystal and/or crystal–matrix interactions. Results suggest that Pn may have a therapeutic potential, since it was able to modify the shape and texture of calculi to a smoother and probably more fragile form, which could contribute to elimination and/or dissolution of calculi.