Download the certificate from your online instance (Settings >> Customizations >> Developer Resources)
Install the certificate into the user certificates:
Search for: Manager User Certificates
Right click on Personal >> Certificates and choose Import.
Browse and select the certificate you downloaded from CRM online
Right click on the certificate “*.crm.dynamics.com” and choose All Tasks >> Export
Choose “Base-64 encoded X.509 (.cer) as the format and click next and export it to a file.
Attach the certificate to CRM.
Open a powershell command window in Admin mode.
Add the CRM powershell snamp in by running: Add-PSSnapin Microsoft.Crm.PowerShell
Next install the certificate by running (replacing the path to the data file with the file from the step where you exported the base-64 file above:
Set-CrmCertificate -certificatetype appfabricissuer -StoreName My -StoreLocation LocalMachine -StoreFindType FindBySubjectDistinguishedName -DataFile C:\base64-crm.dynamics.com.cer
Finally validate that it worked by running: Get-CrmCertificate
More info: