diff --git a/src/bin/juliaup.rs b/src/bin/juliaup.rs
index b585d3b4..d2a2e579 100644
--- a/src/bin/juliaup.rs
+++ b/src/bin/juliaup.rs
@@ -96,7 +96,7 @@ fn main() -> Result<()> {
         Juliaup::Remove { channel } => run_command_remove(&channel, &paths),
         Juliaup::Status {} => run_command_status(&paths),
         Juliaup::Update { channel } => run_command_update(channel, &paths),
-        Juliaup::Gc {} => run_command_gc(&paths),
+        Juliaup::Gc { prune_linked } => run_command_gc(prune_linked, &paths),
         Juliaup::Link {
             channel,
             file,
diff --git a/src/cli.rs b/src/cli.rs
index 14588c55..d665685f 100644
--- a/src/cli.rs
+++ b/src/cli.rs
@@ -33,7 +33,10 @@ pub enum Juliaup {
     /// Show all installed Julia versions
     Status {},
     /// Garbage collect uninstalled Julia versions
-    Gc {},
+    Gc {
+        #[clap(long)]
+        prune_linked: bool,
+    },
     #[clap(subcommand, name = "config")]
     /// Juliaup configuration
     Config(ConfigSubCmd),
diff --git a/src/command_gc.rs b/src/command_gc.rs
index b92eec0d..19c12dd2 100644
--- a/src/command_gc.rs
+++ b/src/command_gc.rs
@@ -3,11 +3,11 @@ use crate::global_paths::GlobalPaths;
 use crate::operations::garbage_collect_versions;
 use anyhow::{Context, Result};
 
-pub fn run_command_gc(paths: &GlobalPaths) -> Result<()> {
+pub fn run_command_gc(prune_linked: bool, paths: &GlobalPaths) -> Result<()> {
     let mut config_file = load_mut_config_db(paths)
         .with_context(|| "`gc` command failed to load configuration data.")?;
 
-    garbage_collect_versions(&mut config_file.data, paths)?;
+    garbage_collect_versions(prune_linked, &mut config_file.data, paths)?;
 
     save_config_db(&mut config_file)
         .with_context(|| "`gc` command failed to save configuration db.")?;
diff --git a/src/command_remove.rs b/src/command_remove.rs
index 7abe52fe..1c743eba 100644
--- a/src/command_remove.rs
+++ b/src/command_remove.rs
@@ -63,7 +63,7 @@ pub fn run_command_remove(channel: &str, paths: &GlobalPaths) -> Result<()> {
     #[cfg(not(windows))]
     remove_symlink(&format!("julia-{}", channel))?;
 
-    garbage_collect_versions(&mut config_file.data, paths)?;
+    garbage_collect_versions(false, &mut config_file.data, paths)?;
 
     save_config_db(&mut config_file).with_context(|| {
         format!(
diff --git a/src/command_update.rs b/src/command_update.rs
index 37081584..ab0d7ff0 100644
--- a/src/command_update.rs
+++ b/src/command_update.rs
@@ -138,7 +138,7 @@ pub fn run_command_update(channel: Option<String>, paths: &GlobalPaths) -> Resul
         }
     };
 
-    garbage_collect_versions(&mut config_file.data, paths)?;
+    garbage_collect_versions(false, &mut config_file.data, paths)?;
 
     save_config_db(&mut config_file)
         .with_context(|| "`update` command failed to save configuration db.")?;
diff --git a/src/operations.rs b/src/operations.rs
index 87aa19db..dde9206b 100644
--- a/src/operations.rs
+++ b/src/operations.rs
@@ -11,6 +11,7 @@ use crate::jsonstructs_versionsdb::JuliaupVersionDB;
 use crate::utils::get_bin_dir;
 use crate::utils::get_julianightlies_base_url;
 use crate::utils::get_juliaserver_base_url;
+use crate::utils::is_valid_julia_path;
 use anyhow::{anyhow, bail, Context, Result};
 use bstr::ByteSlice;
 use bstr::ByteVec;
@@ -602,6 +603,7 @@ pub fn install_non_db_version(
 }
 
 pub fn garbage_collect_versions(
+    prune_linked: bool,
     config_data: &mut JuliaupConfig,
     paths: &GlobalPaths,
 ) -> Result<()> {
@@ -635,6 +637,27 @@ pub fn garbage_collect_versions(
         config_data.installed_versions.remove(&i);
     }
 
+    if prune_linked {
+        let mut channels_to_uninstall: Vec<String> = Vec::new();
+        for (installed_channel, detail) in &config_data.installed_channels {
+            match &detail {
+                JuliaupConfigChannel::LinkedChannel {
+                    command: cmd,
+                    args: _,
+                } => {
+                    if !is_valid_julia_path(&PathBuf::from(cmd)) {
+                        channels_to_uninstall.push(installed_channel.clone());
+                    }
+                }
+                _ => (),
+            }
+        }
+        for channel in channels_to_uninstall {
+            remove_symlink(&format!("julia-{}", &channel))?;
+            config_data.installed_channels.remove(&channel);
+        }
+    }
+
     Ok(())
 }