diff --git a/src/cli/prune.rs b/src/cli/prune.rs
index b89d0e073..dafc861d1 100644
--- a/src/cli/prune.rs
+++ b/src/cli/prune.rs
@@ -5,12 +5,15 @@ use console::style;
 use eyre::Result;
 
 use crate::cli::args::ForgeArg;
+use crate::config::tracking::Tracker;
 use crate::config::{Config, Settings};
 use crate::forge::Forge;
 use crate::toolset::{ToolVersion, ToolsetBuilder};
 use crate::ui::multi_progress_report::MultiProgressReport;
 use crate::ui::prompt;
 
+use super::trust::Trust;
+
 /// Delete unused versions of tools
 ///
 /// mise tracks which config files have been used in ~/.local/share/mise/tracked_config_files
@@ -27,10 +30,39 @@ pub struct Prune {
     /// Do not actually delete anything
     #[clap(long, short = 'n')]
     pub dry_run: bool,
+
+    /// Prune only tracked and trusted configuration links that point to non-existent configurations
+    #[clap(long)]
+    pub configs: bool,
+
+    /// Prune only unused versions of tools
+    #[clap(long)]
+    pub tools: bool,
 }
 
 impl Prune {
     pub fn run(self) -> Result<()> {
+        if self.configs || !self.tools {
+            self.prune_configs()?;
+        }
+        if self.tools || !self.configs {
+            self.prune_tools()?;
+        }
+        Ok(())
+    }
+
+    fn prune_configs(&self) -> Result<()> {
+        if self.dry_run {
+            info!("pruned configuration links {}", style("[dryrun]").bold());
+        } else {
+            Tracker::clean()?;
+            Trust::clean()?;
+            info!("pruned configuration links");
+        }
+        Ok(())
+    }
+
+    fn prune_tools(&self) -> Result<()> {
         let config = Config::try_get()?;
         let ts = ToolsetBuilder::new().build(&config)?;
         let mut to_delete = ts
diff --git a/src/cli/trust.rs b/src/cli/trust.rs
index 48795ae17..9af937ab2 100644
--- a/src/cli/trust.rs
+++ b/src/cli/trust.rs
@@ -1,3 +1,4 @@
+use std::fs::read_dir;
 use std::path::PathBuf;
 
 use clap::ValueHint;
@@ -5,6 +6,8 @@ use eyre::Result;
 
 use crate::config;
 use crate::config::{config_file, DEFAULT_CONFIG_FILENAMES};
+use crate::dirs::TRUSTED_CONFIGS;
+use crate::file::remove_file;
 
 /// Marks a config file as trusted
 ///
@@ -44,6 +47,17 @@ impl Trust {
             self.trust()
         }
     }
+    pub fn clean() -> Result<()> {
+        if TRUSTED_CONFIGS.is_dir() {
+            for path in read_dir(&*TRUSTED_CONFIGS)? {
+                let path = path?.path();
+                if !path.exists() {
+                    remove_file(&path)?;
+                }
+            }
+        }
+        Ok(())
+    }
     fn untrust(&self) -> Result<()> {
         let path = match &self.config_file {
             Some(filename) => PathBuf::from(filename),
diff --git a/src/config/mod.rs b/src/config/mod.rs
index e8b449828..9a45a020f 100644
--- a/src/config/mod.rs
+++ b/src/config/mod.rs
@@ -29,7 +29,7 @@ use crate::{dirs, env, file, forge};
 pub mod config_file;
 mod env_directive;
 pub mod settings;
-mod tracking;
+pub mod tracking;
 
 type AliasMap = BTreeMap<ForgeArg, BTreeMap<String, String>>;
 type ConfigMap = IndexMap<PathBuf, Box<dyn ConfigFile>>;
diff --git a/src/config/tracking.rs b/src/config/tracking.rs
index 32f70b1fe..5b53b8fda 100644
--- a/src/config/tracking.rs
+++ b/src/config/tracking.rs
@@ -21,7 +21,6 @@ impl Tracker {
     }
 
     pub fn list_all() -> Result<Vec<PathBuf>> {
-        Self::clean()?;
         let mut output = vec![];
         for path in read_dir(&*TRACKED_CONFIGS)? {
             let path = path?.path();
@@ -37,10 +36,12 @@ impl Tracker {
     }
 
     pub fn clean() -> Result<()> {
-        for path in read_dir(&*TRACKED_CONFIGS)? {
-            let path = path?.path();
-            if !path.exists() {
-                remove_file(&path)?;
+        if TRACKED_CONFIGS.is_dir() {
+            for path in read_dir(&*TRACKED_CONFIGS)? {
+                let path = path?.path();
+                if !path.exists() {
+                    remove_file(&path)?;
+                }
             }
         }
         Ok(())