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I ran into a similar issue after GoDaddy began issuing new DV TLS certificates from its GoDaddy TLS Root CA – R1 hierarchy.
GoDaddy has moved new DV certificates away from its previous G2 issuing hierarchy. Because the new R1 root is still being distributed to some browser and operating-system trust stores, GoDaddy intends servers to provide an R1-to-G2 cross-signed certificate chain during the transition. This allows clients that do not yet trust the R1 root directly to build the chain back to the already trusted GoDaddy G2 root.
Based on the SSL Labs results posted in this thread, the Azure App Service appears to be serving only:
Domain certificate
└── GoDaddy TLS Intermediate CA DV – R1v1
SSL Labs reports only two certificates being provided. The required GoDaddy TLS Root CA – R1 to G2 Cross Certificate does not appear to be presented, which would explain why Firefox works but Edge and Chrome return ERR_CERT_AUTHORITY_INVALID.
Recommended resolution
Download the following bundle from GoDaddy’s certificate repository:
GoDaddy Certificate Bundle – DV – R1 with Cross to G2, includes Root
GoDaddy Certificate Repository
Direct download: DV R1-to-G2 certificate bundle
The bundle contains the R1 DV intermediate, the R1-to-G2 cross certificate, and the established G2 root.
Rebuild the PFX using the domain certificate as the leaf certificate and the GoDaddy bundle as the additional certificate chain:
openssl pkcs12 -export -out yourdomain-r1.pfx -inkey yourprivate.key -in yourdomain-certificate.crt -certfile gd_bundle_dv-r1-g2.crt.pem
The PFX should contain:Your domain certificate
GoDaddy TLS Intermediate CA DV – R1v1
GoDaddy TLS Root CA – R1 to G2 Cross Certificate
Go Daddy Root Certificate Authority – G2
Upload the rebuilt PFX to Azure App Service, update the TLS binding for the custom domain, and test the site again. GoDaddy specifically states that the complete bundle must be installed rather than only the server certificate, because the bundle provides the alternate trust path needed during the R1 transition.
After rebinding, SSL Labs should show the server providing three certificates:
Domain certificate
└── GoDaddy TLS Intermediate CA DV – R1v1
└── GoDaddy TLS Root CA – R1, cross-signed by G2
The final G2 root normally does not need to be sent by the server because it is already a client trust anchor.
If Azure still provides only two certificates
If the PFX contains the cross-signed certificate but SSL Labs continues to report only two certificates, Azure App Service is likely not presenting the additional cross certificate from the imported PFX. At that point, this should be raised with Azure support as an App Service certificate-chain presentation issue rather than continuing to rebuild the same PFX.
As a diagnostic or temporary workaround on a controlled Windows device, download and install GoDaddy TLS Root CA – R1 into Trusted Root Certification Authorities:
Direct download: GoDaddy TLS Root CA – R1
We resolved the same R1 trust issue in a managed environment by deploying this root certificate through both Group Policy and Intune. Installing the root locally should make Edge and Chrome trust the new hierarchy and can confirm the diagnosis. However, this is only an appropriate permanent solution for managed corporate devices; a public website should provide the complete cross-signed certificate chain so visitors are not required to install a root certificate manually.
GoDaddy references: