India English
Kenya English
United Kingdom English
South Africa English
Nigeria English
United States English
United States Español
Indonesia English
Bangladesh English
Egypt العربية
Tanzania English
Ethiopia English
Uganda English
Congo - Kinshasa English
Ghana English
Côte d’Ivoire English
Zambia English
Cameroon English
Rwanda English
Germany Deutsch
France Français
Spain Català
Spain Español
Italy Italiano
Russia Русский
Japan English
Brazil Português
Brazil Português
Mexico Español
Philippines English
Pakistan English
Turkey Türkçe
Vietnam English
Thailand English
South Korea English
Australia English
China 中文
Somalia English
Canada English
Canada Français
Netherlands Nederlands

Why Your SSL Certificate Keeps Disappearing in IIS and How to Fix It

Securing your website with an SSL certificate is crucial for protecting sensitive data and enhancing visitors’ trust. However, on Windows Servers using Internet Information Services (IIS), you might encounter an irritating problem where your SSL certificate keeps disappearing in IIS. This can disrupt the security of your site and create frustration. In this blog post, we’ll delve into the common causes of this issue and provide step-by-step guidance on how to resolve it.

Understanding the Basics of SSL, IIS, and Server Certificates

SSL Certificates: SSL (Secure Sockets Layer) certificates, and their successor TLS (Transport Layer Security) certificates, are digital files that establish encrypted connections between websites and web browsers. They guarantee the authenticity of your website and safeguard data transmitted over the internet.

IIS: Internet Information Services (IIS) is a powerful web server from Microsoft, designed to host websites and web applications on Windows Servers.

Server Certificates: These are SSL/TLS certificates specifically installed on web servers like IIS. When a visitor accesses your site, the server certificate is used to initiate a secure connection.

Why Does My SSL Certificate Keep Disappearing in IIS?

There are several key reasons why your SSL certificate keeps disappearing in IIS:

  • Missing Private Key: Server certificates work in conjunction with private keys. The private key resides securely on your server. If the SSL certificate is installed without its corresponding private key, it may disappear from the certificate list within IIS, especially after a refresh.
  • Incomplete Certificate Installation: When installing your SSL certificate on your Windows Server, the process may not have been fully completed. The final step of the installation involves completing a certificate request. If you don’t complete the certificate, it might not correctly associate with the private key leading to its disappearance.
  • Issues with the Certificate Store: Windows Servers store SSL certificates within a certificate store. If the certificate store gets corrupted, or the certificate’s permissions are misconfigured, it can lead to disappearing certificates.

Troubleshooting the Disappearing SSL Certificate in IIS

Step 1: Verify the Private Key

  1. Open the Microsoft Management Console (MMC) by pressing Win+R and typing “mmc”.
  2. Navigate to File > Add/Remove Snap-in.
  3. Choose “Certificates” and click Add.
  4. Select Computer Account and then Next.
  5. Choose Local Computer and click Finish.
  6. Click OK to close the “Add/Remove Snap-in” window.
  7. In the MMC, expand Certificates > Personal > Certificates.
  8. Check if the certificate you installed has a little key icon displayed next to it. This icon indicates the presence of a corresponding private key.
  9. If the key icon is missing, you’ll need to locate the private key and either reassociate it with the certificate or request a new certificate.

Step 2: Complete the Certificate Request in IIS

  1. Open the IIS Manager on your IIS server.
  2. Go to Server Certificates.
  3. If you see pending certificate requests, locate the one corresponding to your missing certificate.
  4. Right-click on the request and select Complete Certificate Request.
  5. Provide the path to the certificate file (.cer or .crt) sent by your Certificate Authority (CA).
  6. Give the certificate a friendly name for identification.
  7. Select the appropriate certificate store (usually “Web Hosting”).
  8. Click OK to finish the process.

Step 3: Repair the Certificate Store (If Necessary)

  1. Open a command prompt with administrative privileges.
  2. Type certutil -repairstore my "Serial Number" (replace “Serial Number” with the actual serial number of your certificate).
  3. Press Enter. You might see a confirmation message indicating the repair was successful.

Step 4: Import Certificate as a PFX File (If Required)

If the above steps don’t solve the issue, try importing the certificate along with its private key as a PFX file:

  1. Obtain the private key for your certificate. If you generated the original CSR (Certificate Signing Request), you should have it. Otherwise, contact your Certificate Authority.
  2. Combine the certificate and private key into a single PFX file. You can typically perform this using OpenSSL or tools provided by your Certificate Authority.
  3. Open the MMC again and add the “Certificates” snap-in for the Computer Account.
  4. Right-click on the Personal certificate store and select All Tasks > Import.
  5. Follow the wizard to import the PFX file.

Additional Tips and Considerations

  • Check for Multiple Certificates: If you have multiple certificates with the same domain name, ensure you’re working with the correct one.
  • Verify Certificate Binding: Make sure the certificate is bound to the correct website and port (usually port 443 for HTTPS).
  • Godaddy Specific Note: If you obtained your certificate from GoDaddy, their instructions may require exporting a certificate from their interface, then completing the request in IIS.
  • IIS 10 Considerations: In some instances with IIS 10, you might need to manually refresh the certificate list in IIS after importing a certificate, especially if the private key was located on another server.

Preventing SSL Certificates from Disappearing in the Future

To minimize the chances of your SSL certificate disappearing in IIS again, follow these best practices:

  • Document Your Processes: Maintain thorough documentation outlining the steps involved in obtaining, installing, and renewing SSL certificates on your server.
  • Backup Certificates and Private Keys: Always securely backup your certificates and the corresponding private keys before any major changes to your IIS configuration.
  • Centralize Certificate Management: Consider using a dedicated certificate management tool to streamline the processes and reduce the likelihood of errors.


Encountering a vanishing SSL certificate in IIS can be a perplexing experience. However, by understanding the potential causes and following the troubleshooting steps outlined in this guide, you should be able to effectively resolve this issue and maintain the secure operation of your website.

Have you ever experienced the frustration of a SSL certificate disappearing in IIS? Share your experiences and solutions in the comments section below!

Read also:


Enjoy this blog? Please spread the word :)