Configuring Cloudflare SSL Certificates on Windows Server Core with Powershell

Using Windows Server Core has some big advantages and to our business the advantage is performance since there is no desktop experience. This makes configuring anything you do more complicated if you are not familiar with the equivelent commands in PowerShell. As you would expect there is no way to use the IIS Wizard for completing a Certificate Request and installing the correct certificates needed to server SSL traffic. With a few commands you will have your traffic ready to be served over SSL with Cloudflare.


You have a Windows Server Core (headless) running IIS and you use CloudFlare as your DNS Gateway. There are a lot of benefits to this but let's review some of the requirments of CloudFlare before we get started.

To properly take advantage of the features in CloudFlare you must use the CDN and Proxy setting in the CloudFlare DNS tab. This pushes all of your traffic through CloudFlare first and then it sends it to your server. Using this option gives you lots of additional protection that we aren't going to go into detail here.

Why is this important to understand? 

If you do NOT use the CDN and Proxy in your DNS setting, you will not be able to use the Cloud Flare Origin Certificate because it won't be trusted by the Certificate Authority. It needs to go through their servers to be trusted. 

Just make sure you have the Orange CloudFlare logo on your DNS Entry for the website you are trying to secure

The Process

Before we beging, let's review the steps required to properly set up SSL Bindings on an IIS Web Server with CloudFlare as your DNS Gateway/CDN

  1. Create a Certifacte Signing Request
  2. Create the Origin Certificate on CloudFlare
  3. Import the Origin Certificate on your server
  4. Import the Root Certifacte Authority (CA) from CloudFlare on your server
  5. Update IIS Bindings to use new certificate

Certificate Signing Request

Let's get started by creating our Certificate Signing Request (CSR). This file is needed to supply the correct key information to CloudFlare. RDP (Remote Desktop) onto your server which will show a blank command prompt. Everything we are going to be doing is from Powershell, so launch powershell and we can get started

Creating the CSR has 2 main pieces

  • Info File - Containing information about the CSR
  • certreq.exe - Program to make the actual CSR

CSR Info File (inf)

The info file specifies what type of Certificate Request you are making. You can be explicit with your domain name or use wildcards. In our example here we are going to use a wildcard


Signature= "$Windows NT$"

Subject = "CN=*, OU=Hoefling Software, O=Hoefling Software, L=Rochester, S=New York, C=US"
KeySpec = 1
KeyLength = 2048
Exportable = TRUE
MachineKeySet = TRUE
SMIME = False
PrivateKeyArchive = FALSE
UserProtected = FALSE
UseExistingKeySet = FALSE
ProviderName = "Microsoft RSA SChannel Cryptographic Provider"
ProviderType = 12
RequestType = PKCS10
KeyUsage = 0xa0



Everything in this file should stay the same except your Subject should be updated with your appropraite infomation. Once you have this file generated you are ready to make your CSR!

Create the Certificate Signing Request

After creating the correct info file, navigate to the same directory in powershell. In our example here we created our info file name `ssl.inf`.

certreq -new ssl.inf ssl.req

This command will generate the CSR which will be located in the file `ssl.req`. Opening up the file in notepad is how you are going to get the raw CSR. This is an example of what ours looks like:


We will need this raw string for when we create our Origin Certificate on the CloudFlare Portal

Origin Certificate on CloudFlare

The Certificate Signing Request (CSR) has been generated successfully from our Web Server. It is now time to create our Origin Certificate from the CloudFlare Portal. Once you log in to the portal navigate to the crypto page.

Scroll down on the page to the Origin Certificate section and follow the steps below:

  1. Click on the Create Certificate button to start the wizard
  2. The first step asks if you want CloudFlare to create your CSR or if you have your own. We need to use our CSR so select I have my own private key and CSR
  3. A text field will appear where you will enter the raw CSR we generated earlier. The BEGIN and END lines are required, so copy the ENTIRE .req file that was generated earlier
  4. Verify your hostnames are correct and have the correct wildcards if you specified wildcards
  5. Select the correct validity
  6. Click the Next button

Your Origin Certificate has now been successfully created! Congrats

You should be brought to a screen that has the raw Origin Certificate available for you to copy in the PEM format.

  1. Copy the Certificate Text with the BEGIN and END lines
  2. Go back to your Windows Server where you need to install the Origin Certificate
  3. Open notepad by typing into the console "notepad" and hitting enter
  4. Paste the certificate data into the editor
  5. Save the file as "ssl.cer"

Now we have the certificate file on our Windows Server and it is ready to be imported.

Import Origin Certificate

Back over at our Windows Server we have the certificate file saved and it is ready to be imported. Let's open up powershell and get started.

Our ".cer" file is located at "C:\Users\App\Downloads\ssl.cer". Execute the following commands:

PS C:\> cd Cert:\LocalMachine\my
PS Cert:\LocalMachine\My> Import-Certificate C:\Users\App\Downloads\ssl.cer

When you Import the certificate it will display CloudFlare information which is normal this is a Certificate that is running on their system at the end of the day, they are just allowing you to certify your domain with their infomration. Here is what our output looks like:

Import Root Certificate Authority (CA)

Up to this point we have successfully imported our Origin Certificate onto our server, but a requirment of using CloudFlare for SSL is you need to install the CloudFlare Root Certificate Authority (CA) onto the Windows Server. This is really easy to do, so don't worry too much.

The Root CA was obtained by the CloudFlare docs we copied the certificate we used below to make this easier for you:

Root Certificate Authority (CA)



Follow these steps to properly install the Root Certificate Authority (CA) onto your Windows Server:

  1. Log onto your Windows Server and Launch Powershell
  2. Open up notepad and paste in the Root Certificate Authority (CA) and save it as "cloudflare-root.cer". We saved ours at "C:\Users\App\Downloads\cloudflare-root.cer"
  3. Enter the following commands to properly install it in the root certificate folder
PS C:\> cd Cert:\LocalMachine\root
PS Cert:\LocalMachine\My> Import-Certificate C:\Users\App\Downloads\cloudflare-root.cer

This process should look very familiar to installing the Origin Certificate.

Edit Bindings

Our Windows Server has now been successfully configured correctly! We can update our IIS Bindings to use the new Origin Certificate and serve our traffic over SSL. You can either do this through Remote IIS Management or through powershell. We still like to manage our websites through Remote IIS Management so just edit your bindings like you normally would and test it out:

Test it Out

In our case our new web server is when we navigate to it we should see the secure lock in the browser


That is it!

Now we can start taking advantage of Windows Server Core and serving our websites over SSL with CloudFlare.