A system and method for dynamically protecting against security vulnerabilities in a reconfigurable signal chain. The system includes a signal chain formed from at least a first component connected with a second component. The first component has a set of source outputs and a first authentication block, and the second signal chain component has a set of destination inputs and a second authentication block. The system also includes a signal chain configurator that populates the first authentication block with at least one validated endpoint from the set of destination inputs. A signal chain integrity block, which is communicatively coupled with the first authentication block and the second authentication block, identifies a source-destination pair from one or more endpoint pairs formed from the at least one validated endpoint and the set of source outputs. The signal chain integrity block propagates the source-destination pair to the first authentication block and the second authentication block. The second authentication block authenticates any received input using the source-destination pair.