diff --git a/config.example.toml b/config.example.toml
index 3d5b8c4f..2146bdee 100644
--- a/config.example.toml
+++ b/config.example.toml
@@ -342,6 +342,10 @@
 # Specify the runtime to use for containers (default: "docker", allowed values: "docker", "podman")
 # runtime = "podman"
 
+# Run 'docker system prune' to clean up unused containers, networks, and build cache
+# (default: false)
+# system_prune = false
+
 [lensfun]
 # If disabled, Topgrade invokes `lensfun‑update‑data` without root privilege,
 # then the update will be only available to you. Otherwise, `sudo` is required,
diff --git a/src/config.rs b/src/config.rs
index 65ae0eda..6958c44c 100644
--- a/src/config.rs
+++ b/src/config.rs
@@ -60,6 +60,7 @@ pub struct Containers {
     #[merge(strategy = crate::utils::merge_strategies::vec_prepend_opt)]
     ignored_containers: Option<Vec<String>>,
     runtime: Option<ContainerRuntime>,
+    system_prune: Option<bool>,
 }
 
 #[derive(Deserialize, Default, Debug, Merge)]
@@ -958,6 +959,15 @@ impl Config {
             .unwrap_or(ContainerRuntime::Docker) // defaults to a popular choice
     }
 
+    /// Whether to run system prune for containers.
+    pub fn containers_system_prune(&self) -> bool {
+        self.config_file
+            .containers
+            .as_ref()
+            .and_then(|containers| containers.system_prune)
+            .unwrap_or(false)
+    }
+
     /// Tell whether the specified step should run.
     ///
     /// If the step appears either in the `--disable` command line argument
diff --git a/src/steps/containers.rs b/src/steps/containers.rs
index 462c544c..258a6f00 100644
--- a/src/steps/containers.rs
+++ b/src/steps/containers.rs
@@ -224,7 +224,14 @@ pub fn run_containers(ctx: &ExecutionContext) -> Result<()> {
         }
     }
 
-    if ctx.config().cleanup() {
+    if ctx.config().containers_system_prune() {
+        // Run system prune to clean up unused containers, networks, and build cache
+        if let Err(e) = ctx.execute(&crt).args(["system", "prune", "--force"]).status_checked() {
+            error!("Running system prune failed: {}", e);
+            success = false;
+        }
+    // Only run `image prune` if we don't run `system prune`
+    } else if ctx.config().cleanup() {
         // Remove dangling images
         debug!("Removing dangling images");
         if let Err(e) = ctx.execute(&crt).args(["image", "prune", "-f"]).status_checked() {