In the European Union, SARS-CoV-2 vaccines became available in December 2020. The vaccination campaign in Germany was initially implemented through mass vaccination centers and later joined by general practitioners (GPs) in spring 2021. This study compared population characteristics, perceived access barriers, and satisfaction with the vaccination procedure between vaccination centers and GP practices. A paper-based survey was distributed (07/2021–10/2021) among newly vaccinated individuals in ten GP practices (n = 364) and two vaccine centers (n = 474). Participants in vaccine centers were younger compared to participants in GP practices. GP preference was higher in older participants and those with pre-existing illnesses. Wait time at vaccination site was longer in GP practices, whereas travel distance to site was longer for participants in vaccine centers. However, satisfaction with patient education and recommendation of site were more likely with increasing comprehensibility of the vaccination procedure and physicians’ information as well as perceived sufficiency of patient education duration, factors that can be easily modified by all vaccination sites. Our results demonstrate that both types of vaccination sites complement each other in terms of accessibility and target population and that satisfaction with the vaccination procedure can be promoted at all sites by an easy-to-understand process.