diff --git a/README.md b/README.md
index ae63204..0074fa2 100644
--- a/README.md
+++ b/README.md
@@ -16,6 +16,9 @@ CLOWarden monitors pull requests created in the configuration repository and, wh
 
 Sometimes, however, this may not be enough. Changes can be applied manually to the service bypassing the configuration files (i.e. from the GitHub settings UI), and CLOWarden still needs to make sure that the actual state matches the desired state documented in the configuration files. So in addition to on-demand reconciliation jobs, CLOWarden runs *periodic* ones to ensure everything is all right all the time.
 
+> [!WARNING]
+> Please note that during the reconciliation process, in an attemtp to keep the actual state in sync with the desired state, CLOWarden **will remove** resources **that are not defined** in the configuration file (i.e. teams and permissions, but not repositories). Always make sure that the configuration file represents the actual state (or that you are OK with the changes that will be applied) before enabling the service. The `generate` subcommand of the CLI tool can be helpful to create an initial configuration file from the actual state, whereas the `diff` subcommand can be used to display the differences between the actual and desired state (i.e. what changes will be applied when the service is enabled based on the current configuration file).
+
 ### State
 
 The core piece of state in CLOWarden is the **directory**, which is a catalog that contains **teams** and **users**. The directory is at the disposal of all the services handlers, allowing them to take the appropriate action for each directory change detected. For example, when a new team is added to the directory, the GitHub service handler will create that team on the GitHub organization.
diff --git a/charts/clowarden/README.md b/charts/clowarden/README.md
index 9cf0302..5ffcbc4 100644
--- a/charts/clowarden/README.md
+++ b/charts/clowarden/README.md
@@ -83,6 +83,9 @@ organizations:
 
 CLOWarden includes a CLI tool that can be handy when adding new organizations to your CLOWarden deployment. For more information please see the [repository's README file](https://github.com/cncf/clowarden?#cli-tool).
 
+> [!WARNING]
+> Please note that during the reconciliation process, in an attemtp to keep the actual state in sync with the desired state, CLOWarden **will remove** resources **that are not defined** in the configuration file (i.e. teams and permissions, but not repositories). Always make sure that the configuration file represents the actual state (or that you are OK with the changes that will be applied) before enabling the service. The `generate` subcommand of the CLI tool can be helpful to create an initial configuration file from the actual state, whereas the `diff` subcommand can be used to display the differences between the actual and desired state (i.e. what changes will be applied when the service is enabled based on the current configuration file).
+
 To install the chart with the release name `my-clowarden` run:
 
 ```bash