The introduction of 5G communication capabilities presents additional challenges for the development of products and services that can fully exploit the opportunities offered by high bandwidth, low latency networking. This is particularly relevant to an emerging interest in the Industrial Internet of Things (IIoT), which is a foundation stone of recent technological revolutions such as Digital Manufacturing. A crucial aspect of this is to securely authenticate complex transactions between IIoT devices, whilst marshalling adversarial requests for system authorisation, without the need for a centralised authentication mechanism which cannot scale to the size needed. In this article we combine Physically Unclonable Function (PUF) hardware (using Field Programmable Gate Arrays—FPGAs), together with a multi-layer approach to cloud computing from the National Institute of Standards and Technology (NIST). Through this, we demonstrate an approach to facilitate the development of improved multi-layer authentication mechanisms. We extend prior work to utilise hardware security primitives for adversarial trojan detection, which is inspired by a biological approach to parameter analysis. This approach is an effective demonstration of attack prevention, both from internal and external adversaries. The security is further hardened through observation of the device parameters of connected IIoT equipment. We demonstrate that the proposed architecture can service a significantly high load of device authentication requests using a multi-layer architecture in an arbitrarily acceptable time of less than 1 second.