diff --git a/docs/configuration.md b/docs/configuration.md
index f2a682f2f..d86336359 100644
--- a/docs/configuration.md
+++ b/docs/configuration.md
@@ -313,14 +313,20 @@ If the project is cross-compiled, the architecture of the build and target machi
 If you want to run an activation script inside the environment when either doing a `pixi run` or `pixi shell` these can be defined here.
 The scripts defined in this table will be sourced when the environment is activated using `pixi run` or `pixi shell`
 
+!!! note
+    The activation scripts are run by the system shell interpreter as they run before an environment is available.
+    This means that it runs as `cmd.exe` on windows and `bash` on linux and osx (Unix).
+    Only `.sh`, `.bash` and `.bat` files are supported.
+
+    If you have scripts per platform use the [target](#the-target-table) table.
+
 ```toml
 [activation]
 scripts = ["env_setup.sh"]
+# To support windows platforms as well add the following
+[target.win-64.activation]
+scripts = ["env_setup.bat"]
 ```
-!!! note
-    Specify different scripts for different platforms using the [target](#the-target-table) table
-
-
 
 ## The `target` table
 The target table is a table that allows for platform specific configuration.
diff --git a/src/cli/run.rs b/src/cli/run.rs
index e89f42216..4a7c9cc5a 100644
--- a/src/cli/run.rs
+++ b/src/cli/run.rs
@@ -306,7 +306,19 @@ pub async fn run_activation_async(
     project: &Project,
     prefix: Prefix,
 ) -> miette::Result<HashMap<String, String>> {
-    let additional_activation_scripts = project.activation_scripts(Platform::current())?;
+    let platform = Platform::current();
+    let additional_activation_scripts = project.activation_scripts(platform)?;
+
+    // Check if the platform and activation script extension match. For Platform::Windows the extension should be .bat and for All other platforms it should be .sh or .bash.
+    for script in additional_activation_scripts.iter() {
+        let extension = script.extension().unwrap_or_default();
+        if platform.is_windows() && extension != "bat" {
+            tracing::warn!("The activation script '{}' does not have the correct extension for the platform '{}'. The extension should be '.bat'.", script.display(), platform);
+        } else if !platform.is_windows() && extension != "sh" && extension != "bash" {
+            tracing::warn!("The activation script '{}' does not have the correct extension for the platform '{}'. The extension should be '.sh' or '.bash'.", script.display(), platform);
+        }
+    }
+
     await_in_progress(
         "activating environment",
         run_activation(prefix, additional_activation_scripts.into_iter().collect()),