Crystallization occurs widely in living organisms where different organs could associate with the calcification process, such as the formation of calcium oxalate (CaOx) calculi in the urinary tract. However, the pathogenesis and the role of an inhibitor in the pathological processes involved in urolithiasis is poorly understood. Therefore, the use of phytic acid (PA) as an inhibitor for the organic fibrillar matrix is a novel approach to inhibit the formation of pathological CaOx crystals. Herein, electrospun polymer fiber meshes of polycaprolactone (PCL) with random (R) and aligned (A) fiber orientations containing PA were prepared by electrospinning, and their role as a 3D organic template in in vitro CaOx crystallization was investigated. CaOx crystals were generated on conductive tin indium oxide (ITO)-modified glass with R-PCL and A-PCL fibers in the presence of PA through an electrocrystallization (EC) procedure. This study provides a simple electrochemical approach to evaluate the role of PA as an inhibitor in the nucleation of pathological CaOx crystals. The resulting CaOx crystals were analyzed by chrono-potentiometry, optical microscopy (OM), scanning electron microscopy (SEM), and X-ray diffraction (XRD). We found that PA and the fiber orientations are key factors in the nucleation and crystal growth of CaOx, achieving the stabilization of healthy CaOx crystal and the inhibition of the pathological crystal form.