Purpose The number of pencil beam scanned proton therapy (PBS‐PT) facilities equipped with cone‐beam computed tomography (CBCT) imaging treating thoracic indications is constantly rising. To enable daily internal motion monitoring during PBS‐PT treatments of thoracic tumors, we assess the performance of Motion‐Aware RecOnstructiOn method using Spatial and Temporal Regularization (MA‐ROOSTER) four‐dimensional CBCT (4DCBCT) reconstruction for sparse‐view CBCT data and a realistic data set of patients treated with proton therapy. Methods Daily CBCT projection data for nine non‐small cell lung cancer (NSCLC) patients and one SCLC patient were acquired at a proton gantry system (IBA Proteus® One). Four‐dimensional CBCT images were reconstructed applying the MA‐ROOSTER and the conventional phase‐correlated Feldkamp‐Davis‐Kress (PC‐FDK) method. Image quality was assessed by visual inspection, contrast‐to‐noise ratio (CNR), signal‐to‐noise ratio (SNR), and the structural similarity index measure (SSIM). Furthermore, gross tumor volume (GTV) centroid motion amplitudes were evaluated. Results Image quality for the 4DCBCT reconstructions using MA‐ROOSTER was superior to the PC‐FDK reconstructions and close to FDK images (median CNR: 1.23 PC‐FDK, 1.98 MA‐ROOSTER, and 1.98 FDK; median SNR: 2.56 PC‐FDK, 4.76 MA‐ROOSTER, and 5.02 FDK; median SSIM: 0.18 PC‐FDK vs FDK, 0.31 MA‐ROOSTER vs FDK). The improved image quality of MA‐ROOSTER facilitated GTV contour warping and realistic motion monitoring for most of the reconstructions. Conclusion MA‐ROOSTER based 4DCBCTs performed well in terms of image quality and appear to be promising for daily internal motion monitoring in PBS‐PT treatments of (N)SCLC patients.