The error you’re encountering ModuleInitializeException is related to missing dependencies of the Microsoft.Identity.Web.Certificate package.

• Sometimes, transitive dependencies are not automatically included. You can do this by explicitly adding the missing packages to your project file.

<PackageReference Include="Azure.Security.KeyVault.Secrets" Version="4.4.0" />
<PackageReference Include="Microsoft.Identity.Client.Extensions.Msal" Version="3.0.0" />
<PackageReference Include="Azure.Identity" Version="1.9.0" />

• If you’re deploying the application via Azure DevOps, GitHub Actions, or any CI/CD pipelines, check the build output and ensure that all relevant DLLs are being published to the output directory.
• Makesure that your .csproj file is properly configured to copy all necessary files to the output directory.
• Thanks @Antti K. Koskela for clear explanation I’ve referred this doc and added the below lines to my .csproj file

<PropertyGroup>
 <CopyLocalLockFileAssemblies>true</CopyLocalLockFileAssemblies>
</PropertyGroup>

This setting ensures that all DLLs are copied to the output folder when building locally or in CI/CD.

Now after making the above changes I can see the DLLs in my Azure Web App.