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Once a client certificate is added to the Local Machine account’s Certificates –> Personal –> Certificates through the MMC Certificates snap-in, you can set permissions for service accounts (like Network Service or IIS AppPool\AppPoolIdentityName) with winhttpcertcfg.exe

winhttpcertcfg.exe -g -c LOCAL_MACHINE\My -s “SomeTextFromTheCertSubject” -a “userAccount”

 

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