Abstract Objective. In clinical proton therapy, patient-specific quality assurance (PSQA) is typically performed by using two-dimensional (2D) array detectors placed at two or three selected depths within a phantom. While this method is effective for basic verification, it lacks comprehensive spatial coverage and may miss dose delivery errors in the region with steep dose gradients. This study aims to develop and validate a novel three-dimensional (3D) dosimetry system (PlanDOSE) for full volumetric dose reconstruction from a single treatment delivery, improving the efficiency and accuracy of PSQA in pencil beam scanning (PBS) proton therapy. Approach. PlanDOSE reconstructs 3D dose distributions by real-time monitoring the proton pencil beam using a multi-layer ionization chamber (MLIC) and an integrated dose-position monitoring system (IDPMS). The system was calibrated in detail prior to use, including absolute monitor unit (MU) response, relative channel sensitivity, and water-equivalent thickness (WET) calibration. Its performance was evaluated for multiple intensity modulated proton therapy plans of varying complexities, which includes three standard proton cubes and three clinical plans (brain, lung, liver). Dose distributions reconstructed by PlanDOSE were compared with Eclipse treatment planning system calculations using gamma analysis (2 mm/2%, 10% threshold). Main results. Calibration results showed that PlanDOSE achieved absolute MU measurement errors within ±1%, and inter-channel correction significantly improved the response consistency of MLIC. WET calibration enabled accurate depth-dose curve measurements, with average errors between −1.07% and 2.34%. In dose reconstruction validation, PlanDOSE achieved average gamma passing rates of 98.53% for lateral, 95.40% for depth, and 96.85% for 3D dose distributions. Compared to traditional 2D-based QA dosimetry, PlanDOSE demonstrated higher spatial resolution and better dose fidelity, particularly in regions with steep gradients. Significance. PlanDOSE enables accurate, high-resolution 3D dose verification from a single treatment delivery, offering a more efficient and clinically informative alternative to conventional QA methods, and shows great potential for routine use in PSQA for PBS proton therapy.