Signature-based authentication is used often to authenticate hardware intellectual property (IP) when it is reused on a plug-and-play system-on-chip. A signature embedded in the functional/test component of a hardware IP can easily be verified as it can be generated and observed as functional/scan output of the hardware IP for a certain input key vector. An existing scan-based approach for embedding signature inserts signature through reordering of scan cells in a single scan (SS) chain. However, it is not applicable to the recent reconfigurable scan architectures having reduced test application time. We propose a scheme for embedding two distinct signatures separately in a reconfigurable scan architecture and verifying those without conflict from the packaged chip by using two distinct test modes of the reconfigurable architecture: namely, scan tree mode and SS mode. The two signatures may include one from logic IP source and the other from physical IP source. The overhead in both routing and power has been minimised in our scheme. Experimental results on design overhead and robustness for ISCAS89 benchmarks are very encouraging. © The Institution of Engineering and Technology 2016.