You run Certificate Manager options in sequence to complete a workflow. Several options, for example, generating CSRs, are used in different workflows.

Replace VMCA Root Certificate with Custom Signing Certificate and Replace All Certificates.

This is a single-option workflow (Option 2) can be used by itself, or in the intermediate certificate workflow. See Regenerate a New VMCA Root Certificate and Replace All Certificates.

Make VMCA an Intermediate Certificate Authority

To make VMCA an intermediate CA, you have to run Certificate Manager several times. The workflow gives the complete set of steps for replacing both machine SSL certificates and solution user certificates. It explains what to do in environments with embedded Platform Services Controller or external Platform Services Controller.
  1. To generate a CSR, select Option 2, Replace VMCA Root certificate with Custom Signing Certificate and replace all Certificates. You might have to provide some information about the certificate next. When prompted for an option again, select Option 1.

    Submit the CSR to your external or enterprise CA. You receive a signed certificate and a root certificate from the CA.

  2. Combine the VMCA root certificate with the CA root certificate and save the file.
  3. Select Option 2, Replace VMCA Root certificate with Custom Signing Certificate and replace all Certificates. This process replaces all certificates on the local machine.
  4. In a multi-node deployment, you have to replace certificates on each node.
    1. First you replace the machine SSL certificate with the (new) VMCA certificate (Option 3)
    2. Then you replace the solution user certificates with the (new) VMCA certificate (Option 6).

See Make VMCA an Intermediate Certificate Authority (Certificate Manager)

Replacing All Certificate With Custom Certificates

To replace all certificates with custom certificates, you have to run Certificate Manager several times. The workflow gives the complete set of steps for replacing both machine SSL certificates and solution user certificates. It explains what to do in environments with embedded Platform Services Controller or external Platform Services Controller.
  1. You generate certificate signing requests for the machine SSL certificate and the solution user certificates separately on each machine.
    1. To generate CSRs for the machine SSL certificate, you select Option 1.
    2. If company policy requires that you replace all certificates, you also select Option 5.
  2. After you received the signed certificates and the root certificate from your CA, you replace the machine SSL certificate on each machine by using Option 1.
  3. If you also want to replace the solution user certificates, you select Option 5.
  4. Finally, in a multi-node deployment, you have to repeat the process on each node.

See Replace All Certificates with Custom Certificate (Certificate Manager).

Note: Starting in vSphere 6.5, the following prompt appears when you run the Certificate Manager utility: 
Enter proper value for VMCA 'Name':
Respond to the prompt by entering the fully qualified domain name of the machine on which the certificate configuration is running.