Integration of the Internet of Things (IoT) in the automotive industry has brought benefits as well as security challenges. Significant benefits include enhanced passenger safety and more comprehensive vehicle performance diagnostics. However, current onboard and remote vehicle diagnostics do not include the ability to detect counterfeit parts. A method is needed to verify authentic parts along the automotive supply chain from manufacture through installation and to coordinate part authentication with a secure database. In this study, we develop an architecture for anti-counterfeiting in automotive supply chains. The core of the architecture consists of a cyber-physical trust anchor and authentication mechanisms connected to blockchain-based tracking processes with cloud storage. The key parameters for linking a cyber-physical trust anchor in embedded IoT include identifiers (i.e., serial numbers, special features, hashes), authentication algorithms, blockchain, and sensors. A use case was provided by a two-year long implementation of simple trust anchors and tracking for a coffee supply chain which suggests a low-cost part authentication strategy could be successfully applied to vehicles. The challenge is authenticating parts not normally connected to main vehicle communication networks. Therefore, we advance the coffee bean model with an acoustical sensor to differentiate between authentic and counterfeit tires onboard the vehicle. The workload of secure supply chain development can be shared with the development of the connected autonomous vehicle networks, as the fleet performance is degraded by vehicles with questionable replacement parts of uncertain reliability.