diff --git a/.changes/deep-link-execute-error.md b/.changes/deep-link-execute-error.md
new file mode 100644
index 000000000..dc32c6765
--- /dev/null
+++ b/.changes/deep-link-execute-error.md
@@ -0,0 +1,5 @@
+---
+"deep-link": major
+---
+
+**Breaking:** On Linux, failing to run `xdg-mime` or `update-desktop-database` in `register` and `is_registered` now returns the new `Error::Execute(command, io_error)` variant instead of logging the failure and returning the raw `Error::Io`.
diff --git a/plugins/deep-link/src/error.rs b/plugins/deep-link/src/error.rs
index 41eb764f1..1ef7aa6ba 100644
--- a/plugins/deep-link/src/error.rs
+++ b/plugins/deep-link/src/error.rs
@@ -23,21 +23,15 @@ pub enum Error {
     #[cfg(target_os = "linux")]
     #[error(transparent)]
     ParseIni(#[from] ini::ParseError),
+    /// Failed to run an OS command such as `xdg-mime` or `update-desktop-database`.
+    #[cfg(target_os = "linux")]
+    #[error("Failed to run OS command `{0}`: {1}")]
+    Execute(&'static str, #[source] std::io::Error),
     #[cfg(mobile)]
     #[error(transparent)]
     PluginInvoke(#[from] tauri::plugin::mobile::PluginInvokeError),
 }
 
-// TODO(v3): change this into an error in v3,
-// see <https://github.com/tauri-apps/plugins-workspace/pull/2970#issuecomment-3244660138>.
-#[inline]
-#[cfg(target_os = "linux")]
-pub(crate) fn inspect_command_error<'a>(command: &'a str) -> impl Fn(&std::io::Error) + 'a {
-    move |e| {
-        tracing::error!("Failed to run OS command `{command}`: {e}");
-    }
-}
-
 impl Serialize for Error {
     fn serialize<S>(&self, serializer: S) -> std::result::Result<S::Ok, S::Error>
     where
diff --git a/plugins/deep-link/src/lib.rs b/plugins/deep-link/src/lib.rs
index b60ca810f..574a79881 100644
--- a/plugins/deep-link/src/lib.rs
+++ b/plugins/deep-link/src/lib.rs
@@ -351,14 +351,12 @@ mod imp {
                 Command::new("update-desktop-database")
                     .arg(target)
                     .status()
-                    .inspect_err(crate::error::inspect_command_error(
-                        "update-desktop-database",
-                    ))?;
+                    .map_err(|error| crate::Error::Execute("update-desktop-database", error))?;
 
                 Command::new("xdg-mime")
                     .args(["default", &file_name, mime_type.as_str()])
                     .status()
-                    .inspect_err(crate::error::inspect_command_error("xdg-mime"))?;
+                    .map_err(|error| crate::Error::Execute("xdg-mime", error))?;
 
                 Ok(())
             }
@@ -463,7 +461,7 @@ mod imp {
                         &format!("x-scheme-handler/{}", _protocol.as_ref()),
                     ])
                     .output()
-                    .inspect_err(crate::error::inspect_command_error("xdg-mime"))?;
+                    .map_err(|error| crate::Error::Execute("xdg-mime", error))?;
 
                 Ok(String::from_utf8_lossy(&output.stdout).contains(&file_name))
             }