To achieve an accurate stopping power ratio (SPR) prediction in particle therapy treatment planning, we previously proposed a simple conversion to the SPR from dual-energy (DE) computed tomography (CT) data via electron density and effective atomic number (Z eff) calibration (DEEDZ-SPR). This study was conducted to carry out an initial implementation of the DEEDZ-SPR conversion method with a clinical treatment planning system (TPS; VQA, Hitachi Ltd., Tokyo) for proton beam therapy. Consequently, this paper presents a proton therapy plan for an anthropomorphic phantom to evaluate the stability of the dose calculations obtained by the DEEDZ-SPR conversion against the variation of the calibration phantom size. Dual-energy x-ray CT images were acquired using a dual-source CT (DSCT) scanner. A single-energy CT (SECT) scan using the same DSCT scanner was also performed to compare the DEEDZ-SPR conversion with the SECT-based SPR (SECT-SPR) conversion. The scanner-specific parameters necessary for the SPR calibration were obtained from the CT images of tissue substitutes in a calibration phantom. Two calibration phantoms with different sizes (a 33 cm diameter phantom and an 18 cm diameter phantom) were used for the SPR calibrations to investigate the beam-hardening effect on dosimetric uncertainties. Each set of calibrated SPR data was applied to the proton therapy plan designed using the VQA TPS with a pencil beam algorithm for the anthropomorphic phantom. The treatment plans with the SECT-SPR conversion exhibited discrepancies between the dose distributions and the dose-volume histograms (DVHs) of the 33 cm and 18 cm phantom calibrations. In contrast, the corresponding dose distributions and the DVHs obtained using the DEEDZ-SPR conversion method coincided almost perfectly with each other. The DEEDZ-SPR conversion appears to be a promising method for providing proton dose plans that are stable against the size variations of the calibration phantom and the patient.