diff --git a/crates/automation/src/headless.rs b/crates/automation/src/headless.rs
index 684cb316bd..736c4d2901 100644
--- a/crates/automation/src/headless.rs
+++ b/crates/automation/src/headless.rs
@@ -142,10 +142,15 @@ impl Headless {
                 warnings
             }
         };
-        let is_native = format
-            .map(|f| f.trim_start_matches('.').eq_ignore_ascii_case("pcraft"))
-            .unwrap_or_else(|| target.extension().is_some_and(|e| e.eq_ignore_ascii_case("pcraft")));
-        if is_native {
+        // A layered document save (PSD, PSB or .pcraft) is a full write, not a flattened copy:
+        // record the current revision as saved so the session stops reporting `dirty`, and make
+        // the file the document's path. A flat export (PNG, JPEG, …) is a copy and leaves both
+        // alone (#1547).
+        let ext = format
+            .map(|f| f.trim_start_matches('.').to_ascii_lowercase())
+            .or_else(|| target.extension().map(|e| e.to_string_lossy().to_ascii_lowercase()));
+        let layered = matches!(ext.as_deref(), Some("psd" | "psb")) || ext.as_deref() == Some(photocraft_format::EXTENSION);
+        if layered {
             // Saving by index must not retarget the next automation command.
             let previously_active = self.session.active_index();
             self.session.set_active(i);
diff --git a/crates/automation/tests/layered_save_dirty.rs b/crates/automation/tests/layered_save_dirty.rs
new file mode 100644
index 0000000000..0a19277f40
--- /dev/null
+++ b/crates/automation/tests/layered_save_dirty.rs
@@ -0,0 +1,82 @@
+//! Regression for #1547: a successful save back to the document's own PSD or PSB file must
+//! record the current revision as saved, so the session stops reporting `dirty` (as `.pcraft`
+//! already did). A flat export stays a copy and leaves the dirty state and path alone.
+
+use photocraft_automation::Headless;
+use serde_json::json;
+
+fn tmp(name: &str) -> std::path::PathBuf {
+    let dir = std::env::temp_dir().join(format!(
+        "pc-layered-save-{name}-{}-{}",
+        std::process::id(),
+        std::time::SystemTime::now().duration_since(std::time::UNIX_EPOCH).unwrap().as_nanos()
+    ));
+    std::fs::create_dir_all(&dir).unwrap();
+    dir
+}
+
+/// The issue's scenario: create `name`, reopen it, edit, then save with no path. The save writes
+/// the document's own file and must clear `dirty`.
+fn pathless_save_clears_dirty(dir: &std::path::Path, name: &str) {
+    let path = dir.join(name);
+    let mut headless = Headless::trusted_local();
+    headless.handle("doc.new", json!({"width": 8, "height": 8, "background": "white"})).unwrap();
+    headless.handle("doc.save", json!({"path": path.to_str().unwrap()})).unwrap();
+    assert!(path.is_file(), "{name} was written");
+
+    // Reopen the saved file and edit it, so the pathless save below writes back over its own file.
+    headless.handle("doc.open", json!({"path": path.to_str().unwrap()})).unwrap();
+    headless.handle("engine.execute", json!({"command": "image.adjustments.invert", "params": {}})).unwrap();
+    assert!(headless.session.active().unwrap().is_dirty(), "{name}: the edit dirties");
+
+    // The reported symptom: the save succeeds but the session still reports `dirty`.
+    headless.handle("doc.save", json!({})).unwrap();
+    assert!(!headless.session.active().unwrap().is_dirty(), "{name}: a pathless save is clean");
+    let revision = headless.session.active().unwrap().revision;
+    assert_eq!(headless.session.active().unwrap().saved_revision, revision, "{name}: the current revision is recorded");
+    assert_eq!(headless.session.active().unwrap().path.as_deref(), path.to_str(), "{name}: the file is still the path");
+
+    // A second save, with no further edit, stays clean.
+    headless.handle("doc.save", json!({})).unwrap();
+    assert!(!headless.session.active().unwrap().is_dirty(), "{name}: a repeat save stays clean");
+
+    let bytes = std::fs::read(&path).unwrap();
+    if name.ends_with("psd") {
+        assert!(photocraft_io::is_psd(&bytes), "{name}: PSD magic");
+    } else {
+        assert_eq!(&bytes[..4], b"8BPS", "{name}: PSB magic");
+    }
+}
+
+#[test]
+fn pathless_psd_and_psb_saves_clear_dirty() {
+    let dir = tmp("clean");
+    pathless_save_clears_dirty(&dir, "a.psd");
+    pathless_save_clears_dirty(&dir, "a.psb");
+    std::fs::remove_dir_all(dir).unwrap();
+}
+
+/// The control from the issue: exporting a flat copy is not a document save, so it must neither
+/// clear `dirty` nor retarget the document's path. A `.pcraft` save sets the path on both the old
+/// and the new code, so this test isolates the flat-export behaviour.
+#[test]
+fn a_flat_export_is_a_copy_and_leaves_the_document_dirty() {
+    let dir = tmp("copy");
+    let native = dir.join("doc.pcraft");
+    let png = dir.join("copy.png");
+    let mut headless = Headless::trusted_local();
+    headless.handle("doc.new", json!({"width": 8, "height": 8, "background": "white"})).unwrap();
+    headless.handle("doc.save", json!({"path": native.to_str().unwrap()})).unwrap();
+    headless.handle("engine.execute", json!({"command": "image.adjustments.invert", "params": {}})).unwrap();
+    assert!(headless.session.active().unwrap().is_dirty(), "the edit dirties");
+
+    headless.handle("doc.save", json!({"path": png.to_str().unwrap()})).unwrap();
+    assert!(png.is_file(), "the PNG copy was written");
+    assert!(headless.session.active().unwrap().is_dirty(), "a flat export leaves the document dirty");
+    assert_eq!(headless.session.active().unwrap().path.as_deref(), native.to_str(), "the path is not retargeted to the copy");
+
+    // ...and the document can still be saved back to its own native file.
+    headless.handle("doc.save", json!({})).unwrap();
+    assert!(!headless.session.active().unwrap().is_dirty());
+    std::fs::remove_dir_all(dir).unwrap();
+}
\ No newline at end of file
diff --git a/docs/control-protocol.md b/docs/control-protocol.md
index 6dcbbb3086..631cc4e987 100644
--- a/docs/control-protocol.md
+++ b/docs/control-protocol.md
@@ -275,7 +275,7 @@ no MCP framing, no app start-up per command. Configure its file access with the
 | `engine.commands` | `{filter?}`: registry with params docs and enablement |
 | `session.list` | open documents and the active index |
 | `doc.open` / `doc.new` | `{path}` / `file.new` params |
-| `doc.save` | `{path?, format?, quality?, index?}` (`.pcraft` native, else export by extension). Without `path` only a PSD, PSB or `.pcraft` document is written back to its own file, in its own format; anything else is an error and the file is left unchanged |
+| `doc.save` | `{path?, format?, quality?, index?}` (`.pcraft` native, else export by extension). Without `path` only a PSD, PSB or `.pcraft` document is written back to its own file, in its own format; anything else is an error and the file is left unchanged. A successful layered save (PSD, PSB or `.pcraft`) records the current revision as saved and makes the file the document's path, so `session.list` reports `dirty: false`; a flat export is a copy and leaves the document dirty |
 | `doc.inspect` | `{index?}`: same JSON as `document.inspect` |
 | `doc.render` | `{index?, maxSide? (1024; 0 = full), path?}`: PNG to `path`, else `{mime, base64}` |
 | `doc.select` / `doc.close` | `{index}` / `{index?}` |