@Jamie Brandwood Conditional access policy cannot be applied if you are requesting token under application context i.e., using client credentials.
There is an active feedback regarding this feature here: https://feedback.azure.com/forums/169401-azure-active-directory/suggestions/37867180-restricting-access-of-azure-service-principals-u. Please vote here as this is monitored by MS product team and based on the popularity of the idea features are added to Azure.
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