diff --git a/src/git_changes.rs b/src/git_changes.rs
index a795a7c..069b525 100644
--- a/src/git_changes.rs
+++ b/src/git_changes.rs
@@ -121,7 +121,12 @@ async fn get_changed_files_bitcoin_core(pr_number: Option<u32>) -> Result<Vec<St
         Err(_) if used_remote == "upstream" => {
             // If upstream diff failed, try origin
             println!("Diff with upstream/master failed, trying origin/master...");
-            let diff_args_origin = &["diff", "--name-only", "origin/master...HEAD"];
+            let diff_args_origin = &[
+                "diff",
+                "--name-only",
+                "--diff-filter=d",
+                "origin/master...HEAD",
+            ];
             run_git_command(diff_args_origin).await
         }
         Err(e) => Err(e),
diff --git a/src/mutation.rs b/src/mutation.rs
index 7650657..a40c425 100644
--- a/src/mutation.rs
+++ b/src/mutation.rs
@@ -25,6 +25,10 @@ fn build_config_json(range_lines: Option<(usize, usize)>) -> Option<String> {
     range_lines.map(|(start, end)| format!("{{\"range\":[{},{}]}}", start, end))
 }
 
+fn should_mutate_changed_file(project: Project, file_path: &str) -> bool {
+    !project.should_skip_file(file_path) && Path::new(file_path).is_file()
+}
+
 pub async fn run_mutation(
     project: Project,
     pr_number: Option<u32>,
@@ -93,7 +97,9 @@ pub async fn run_mutation(
         for file_changed in files_changed {
             // Skip non-source files (docs, tooling, benchmarks, ...).
             // The exact set is project-specific; see `Project::should_skip_file`.
-            if project.should_skip_file(&file_changed) {
+            // Also skip deleted/missing files so PR mutation only targets files
+            // that can actually be read in the checked-out worktree.
+            if !should_mutate_changed_file(project, &file_changed) {
                 continue;
             }
 
@@ -565,6 +571,31 @@ mod tests {
         assert_eq!(content, "test/file.cpp");
     }
 
+    #[test]
+    fn test_should_mutate_changed_file_requires_existing_source_file() {
+        let temp_dir = tempdir().unwrap();
+        let source_file = temp_dir.path().join("src/node.cpp");
+        fs::create_dir_all(source_file.parent().unwrap()).unwrap();
+        fs::write(&source_file, "int value = 1;\n").unwrap();
+
+        let doc_file = temp_dir.path().join("doc/example.cpp");
+        fs::create_dir_all(doc_file.parent().unwrap()).unwrap();
+        fs::write(&doc_file, "int value = 1;\n").unwrap();
+
+        assert!(should_mutate_changed_file(
+            Project::BitcoinCore,
+            source_file.to_str().unwrap()
+        ));
+        assert!(!should_mutate_changed_file(
+            Project::BitcoinCore,
+            temp_dir.path().join("src/deleted.cpp").to_str().unwrap()
+        ));
+        assert!(!should_mutate_changed_file(
+            Project::BitcoinCore,
+            doc_file.to_str().unwrap()
+        ));
+    }
+
     #[test]
     fn test_write_mutation() {
         let temp_dir = tempdir().unwrap();