Various methods and systems for autonomously upgrading deployed resources in a distributed computing environment are provided. An autonomous upgrade system identifies updates such as operating system image updates and virtual machine extension updates for deployment in the distributed computing environment. The autonomous upgrade system identifies eligible tenants, identifies deployed resources that may be impacted by the identified update, batches the resources and upgrades the batched resources. The autonomous upgrade system performs a diagnostic test on upgraded resources to determine whether an upgrade was successful. In some embodiments, the diagnostic test is performed by executing a diagnostic script that can be provided by a tenant. The autonomous upgrade system can stop or pause the upgrade if various success metrics are not satisfied. In some embodiments, the autonomous upgrade system tests and certifies newly published updates for deployment to the distributed computing environment.