Let's Encrypt windows clients with IIS cannot handle multiple websites?

I’m running a VM with windows server 2012 R2 and IIS 8.5 and I have multiple websites configured (on the same IP) and multiple subdomain-websites. I tried running Certify and Let’s Encrypt Win Simple, but the same problem occurs for both.

When I select 1 website to create a cert. and update the IIS bindings it works fine, but when I continue to the 2nd website, it works again, but then it also removes the binding from the first website again, and updates it to the same binding as the 2nd website. It seems that I cannot get multiple certificates with each unique bindings in IIS, resulting in that I can only get LE to work with 1 website at any time.

Any ideas?

When you are adding the bindings are you ensuring you select the option “Require Server Name Indication” ?

I didn’t, because some of our webservices don’t work with SAN

SAN and SNI are two different things, it’s the way you have it setup though ( not using SNI) for those websites which prevents you using different certs for different websites.

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