Create a Certificate Request from your Windows Server
Open Internet Information Services (IIS) Manager from the Windows Server 2016 through Control Panel -> Administrative Tools
Select your server from the Connections and open Server Certificates
From the Server Certificates Actions select Create Certificate Request
Fill in the following form with your details:
Common name: [your domain]
Organization: [your organization name]
etc.
Set the settings for the Cryptographic service provider of the certificate, the bigger the length of the certificate the better the security but it makes the server slower.
Specify the filename of the txt file where you will save the certificate request
Create the certificate from Cloudflare using your own certificate request that you created from your Windows Server
Open your Cloudflare account, select your domain, open SSL/TLS tab and click on Origin Server in order to create the certificate
Select the option ‘I have my own private key and CSR’ where you will Copy-Paste the certificate you saved on the txt file from your Windows Server, fill in the hostnames, select the expiration years and press Next
Copy-Paste in PEM key format the certificate in a text file and save the file
Add the public certificate from Cloudflare at your Windows Server
Copy the file with the PEM certificate from Cloudflare at your Windows Server
Select ‘Complete Certificate Request’ from the IIS Manager Server Certificates Actions
Select the PEM certificate you copied at the server and add a friendly name (e.g. the domain it covers and the expiration date of it):
The certificate will appear at the list of the Server Certificates with the Friendly name you added at the form before
Import Cloudflare Origin CA root certificate at your Windows server
Copy the Cloudflare Origin CA — RSA Root certificate from Cloudflare website, save to a file and transfer it to your Windows Server
Open the Certificates Microsoft Management Console (MMC) snap-in by typing mmc.exe at the command prompt (or at the run dialog that you can open by pressing the buttons Win+R)
On the File menu, select Add/Remove Snap-in
In the Add or Remove Snap-ins dialog box, select Certificates snap-in in the Available snap-ins list, click Add, and then select OK
In the Certificates snap-in dialog-box, select Computer account, and then select Next
In the Select computer dialog box, click on Finish
In the Add or Remove Snap-ins dialog box, select OK
In the Certificates MMC snap-in, expand Certificates, right-click Intermediate Certification Authorities, point to All Tasks, and then select Import
In the Certificate Import Wizard, select Next
In the File to Import page, select the file with the Cloudflare origin CA root certificate you saved before, and then select Next
Select Next at the Certificate Import Wizard
Select Finish at the Certificate Import Wizard
The certificate will appear at the Certificates list
Use the newly created server origin certificate from Cloudflare for your website
Select Bindings from the IIS Manager Web Site Actions
Select the https binding and click Edit. If you do not have an https binding, press Add... to create one like in the second screen down
At the SSL certificate dropdown list Select the new certificate and press OK
Force your website domain to pass through Cloudflare
Open your Cloudflare account, select your domain, go to DNS option and change the Proxy status for your website from DNS only to Proxied by click it
Enable Cloudflare full (strict) SSL TLS encryption mode in the SSL/TLS tab
