Purpose: Cone beam computed tomography (CBCT) suffers from a large amount of scatter, resulting in severe scatter artifacts in the reconstructions. Recently, a new scatter correction approach, called improved primary modulator scatter estimation (iPMSE), was introduced. That approach utilizes a primary modulator that is inserted between the X-ray source and the object. This modulation enables estimation of the scatter in the projection domain by optimizing an objective function with respect to the scatter estimate. Up to now the approach has not been implemented on a clinical angiography C-arm CT system. Methods: In our work, the iPMSE method is transferred to a clinical C-arm CBCT. Additional processing steps are added in order to compensate for the C-arm scanner motion and the automatic X-ray tube current modulation. These challenges were overcome by establishing a reference modulator database and a block-matching algorithm. Experiments with phantom and experimental in vivo data were performed to evaluate the method. Results: We show that scatter correction using primary modulation is possible on a clinical C-arm CBCT. Scatter artifacts in the reconstructions are reduced with the newly extended method. Compared to a scan with a narrow collimation, our approach showed superior results with an improvement of the contrast and the contrast-to-noise ratio for the phantom experiments. In vivo data are evaluated by comparing the results with a scan with a narrow collimation and with a constant scatter correction approach. Conclusions: Scatter correction using primary modulation is possible on a clinical CBCT by compensating for the scanner motion and the tube current modulation. Scatter artifacts could be reduced in the reconstructions of phantom scans and in experimental in vivo data.