diff --git a/src/cli/parameters.rs b/src/cli/parameters.rs
index 21d216d..d23de05 100644
--- a/src/cli/parameters.rs
+++ b/src/cli/parameters.rs
@@ -18,6 +18,9 @@ pub(crate) enum Commands {
     /// Run a single build.
     Build(BuildArgs),
 
+    /// Clean up builds.
+    Clean(CleanArgs),
+
     /// Launch a daemon to run builds.
     Daemon(DaemonArgs),
 
@@ -36,6 +39,13 @@ pub(crate) struct BuildArgs {
     pub(crate) target: Vec<String>,
 }
 
+#[derive(Args, Debug)]
+pub(crate) struct CleanArgs {
+    /// Path to the nix_builder config file.
+    #[arg(short, long)]
+    pub(crate) config: PathBuf,
+}
+
 #[derive(Args, Debug)]
 pub(crate) struct DaemonArgs {
     /// Path to the nix_builder config file.
diff --git a/src/command/clean/mod.rs b/src/command/clean/mod.rs
new file mode 100644
index 0000000..ac12c0d
--- /dev/null
+++ b/src/command/clean/mod.rs
@@ -0,0 +1,3 @@
+mod runner;
+
+pub(crate) use runner::run_clean;
diff --git a/src/command/clean/runner.rs b/src/command/clean/runner.rs
new file mode 100644
index 0000000..2b2c348
--- /dev/null
+++ b/src/command/clean/runner.rs
@@ -0,0 +1,43 @@
+use std::collections::HashSet;
+
+use tracing::info;
+
+use crate::Result;
+use crate::cli::parameters::CleanArgs;
+use crate::config::Config;
+
+pub(crate) async fn run_clean(args: CleanArgs) -> Result<()> {
+    let config = Config::load_from_file(args.config).await?;
+
+    let target_directory = config.get_target_root_directory()?;
+    let existing_target_names = {
+        let mut existing_entries = tokio::fs::read_dir(&target_directory).await?;
+        let mut existing_target_names = HashSet::new();
+        while let Some(existing_target) = existing_entries.next_entry().await? {
+            existing_target_names.insert(existing_target.file_name());
+        }
+        existing_target_names
+    };
+
+    let configured_target_names = config
+        .get_target_configs()
+        .iter()
+        .map(|target| {
+            target
+                .get_target_directory(&config)
+                .and_then(|target_path| {
+                    target_path
+                        .file_name()
+                        .map(|name| name.to_os_string())
+                        .ok_or("Entry with no file name in target directory.".into())
+                })
+        })
+        .collect::<Result<HashSet<_>>>()?;
+
+    for dir in existing_target_names.difference(&configured_target_names) {
+        info!("DELETE TARGET: {:?}", dir);
+        tokio::fs::remove_dir_all(target_directory.join(dir)).await?;
+    }
+
+    Ok(())
+}
diff --git a/src/command/mod.rs b/src/command/mod.rs
index d783347..c7ed7e5 100644
--- a/src/command/mod.rs
+++ b/src/command/mod.rs
@@ -1,3 +1,4 @@
 pub(crate) mod build;
+pub(crate) mod clean;
 pub(crate) mod daemon;
 pub(crate) mod feed_logs;
diff --git a/src/config/root.rs b/src/config/root.rs
index 6f6d0be..7e447c6 100644
--- a/src/config/root.rs
+++ b/src/config/root.rs
@@ -63,6 +63,10 @@ impl Config {
         Ok(target_config)
     }
 
+    pub(crate) fn get_target_configs(&self) -> &Vec<TargetConfig> {
+        &self.targets
+    }
+
     /// The root directory where all the output is stored.
     pub(crate) fn get_output_directory(&self) -> Result<Cow<'_, Path>, CustomError> {
         let maybe_repo_directory = self.output_directory.as_deref().map(Cow::Borrowed);
@@ -80,4 +84,20 @@ impl Config {
         let database_path = output_directory.join("nix_builder.sqlite");
         Ok(Cow::Owned(database_path))
     }
+
+    /// The folder that contains the folders for the build targets.
+    pub(crate) fn get_target_root_directory<'target>(
+        &'target self,
+    ) -> Result<Cow<'target, Path>, CustomError> {
+        let output_directory = self.get_output_directory()?;
+        Ok(Cow::Owned(output_directory.join("target")))
+    }
+
+    /// The folder that contains the folders containing the checkouts of the git repositories.
+    pub(crate) fn get_repo_root_directory<'target>(
+        &'target self,
+    ) -> Result<Cow<'target, Path>, CustomError> {
+        let output_directory = self.get_output_directory()?;
+        Ok(Cow::Owned(output_directory.join("repo")))
+    }
 }
diff --git a/src/config/target.rs b/src/config/target.rs
index 11452dd..f65847f 100644
--- a/src/config/target.rs
+++ b/src/config/target.rs
@@ -36,33 +36,15 @@ pub(crate) struct TargetConfig {
 }
 
 impl TargetConfig {
-    /// The folder that contains the folders for the build targets.
-    pub(crate) fn get_target_root_directory<'target, 'root>(
-        &'target self,
-        config_root: &'root Config,
-    ) -> Result<Cow<'target, Path>, CustomError> {
-        let output_directory = config_root.get_output_directory()?;
-        Ok(Cow::Owned(output_directory.join("target")))
-    }
-
     /// The root directory for this specific build target.
     pub(crate) fn get_target_directory<'target, 'root>(
         &'target self,
         config_root: &'root Config,
     ) -> Result<Cow<'target, Path>, CustomError> {
-        let target_root = self.get_target_root_directory(config_root)?;
+        let target_root = config_root.get_target_root_directory()?;
         Ok(Cow::Owned(target_root.join(&self.name)))
     }
 
-    /// The folder that contains the folders containing the checkouts of the git repositories.
-    pub(crate) fn get_repo_root_directory<'target, 'root>(
-        &'target self,
-        config_root: &'root Config,
-    ) -> Result<Cow<'target, Path>, CustomError> {
-        let output_directory = config_root.get_output_directory()?;
-        Ok(Cow::Owned(output_directory.join("repo")))
-    }
-
     /// The root of the checkout of the git repository.
     pub(crate) fn get_repo_directory<'target, 'root>(
         &'target self,
@@ -71,7 +53,7 @@ impl TargetConfig {
         let hashed_repo = Sha256::digest(&self.repo);
         let hashed_repo = hex_string(&hashed_repo);
 
-        let repo_root = self.get_repo_root_directory(config_root)?;
+        let repo_root = config_root.get_repo_root_directory()?;
         Ok(Cow::Owned(repo_root.join(hashed_repo)))
     }
 
diff --git a/src/main.rs b/src/main.rs
index b184aee..9fbad30 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -9,6 +9,7 @@ use clap::Parser;
 use self::cli::parameters::Cli;
 use self::cli::parameters::Commands;
 use self::command::build::run_build;
+use self::command::clean::run_clean;
 use self::command::daemon::start_daemon;
 use self::command::feed_logs::feed_logs;
 use self::error::CustomError;
@@ -38,6 +39,9 @@ async fn main_body() -> Result<ExitCode> {
         Commands::Build(args) => {
             run_build(args).await?;
         }
+        Commands::Clean(args) => {
+            run_clean(args).await?;
+        }
         Commands::Daemon(args) => {
             start_daemon(args).await?;
         }