Scan-based test is commonly used to increase testability and fault coverage, however, it is also known to be a liability for chip security. Research has shown that intellectual property (IP) or secret keys can be leaked through scan-based attacks, which can be performed by entities within the supply chain. In this paper, we propose a design and test methodology against scan-based attacks throughout the supply chain, which includes a dynamically obfuscated scan (DOS) for protecting IP/integrated circuits (ICs). By perturbing test patterns/responses and protecting the Obfuscation Key, the proposed architecture is proven to be robust against existing noninvasive scan-based attacks, and can protect all scan data from attackers in foundry, assembly, and system development without compromising the testability. Further, a novel test methodology cooperating with the DOS design is also proposed, which shows full pattern application flexibility. Finally, detailed security and experimental analyses have been performed on ITC and industrial benchmarks. Demonstrated by the simulation results, the proposed architecture can be easily plugged into EDA generated scan chains without generating a noticeable impact on conventional IC design, manufacturing, and test flow. The results demonstrate that the proposed methodology can protect chips from existing brute force, differential, and other scan-based attacks that target the Obfuscation Key. Furthermore, the proposed design is of low overhead on area, power consumption, and pattern generation time, and there is no impact on test time.