diff --git a/src/Cli/Microsoft.DotNet.FileBasedPrograms/FileLevelDirectiveHelpers.cs b/src/Cli/Microsoft.DotNet.FileBasedPrograms/FileLevelDirectiveHelpers.cs
index 1157bc586313..0dcd623c93d4 100644
--- a/src/Cli/Microsoft.DotNet.FileBasedPrograms/FileLevelDirectiveHelpers.cs
+++ b/src/Cli/Microsoft.DotNet.FileBasedPrograms/FileLevelDirectiveHelpers.cs
@@ -258,7 +258,8 @@ internal readonly record struct SourceFile(string Path, SourceText Text)
     public static SourceFile Load(string filePath)
     {
         using var stream = File.OpenRead(filePath);
-        return new SourceFile(filePath, SourceText.From(stream, Encoding.UTF8));
+        // Let SourceText.From auto-detect the encoding (including BOM detection)
+        return new SourceFile(filePath, SourceText.From(stream, encoding: null));
     }
 
     public SourceFile WithText(SourceText newText)
@@ -269,7 +270,9 @@ public SourceFile WithText(SourceText newText)
     public void Save()
     {
         using var stream = File.Open(Path, FileMode.Create, FileAccess.Write);
-        using var writer = new StreamWriter(stream, Encoding.UTF8);
+        // Use the encoding from SourceText, which preserves the original BOM state
+        var encoding = Text.Encoding ?? new UTF8Encoding(encoderShouldEmitUTF8Identifier: false);
+        using var writer = new StreamWriter(stream, encoding);
         Text.Write(writer);
     }
 
diff --git a/test/dotnet.Tests/CommandTests/Run/FileBasedAppSourceEditorTests.cs b/test/dotnet.Tests/CommandTests/Run/FileBasedAppSourceEditorTests.cs
index f6b181615b72..b34ce92dfd96 100644
--- a/test/dotnet.Tests/CommandTests/Run/FileBasedAppSourceEditorTests.cs
+++ b/test/dotnet.Tests/CommandTests/Run/FileBasedAppSourceEditorTests.cs
@@ -517,6 +517,94 @@ public void RemoveMultiple()
             """));
     }
 
+    /// <summary>
+    /// Verifies that files without UTF-8 BOM don't get one added when saved.
+    /// This is critical for shebang (#!) scripts on Unix-like systems.
+    /// <see href="https://github.com/dotnet/sdk/issues/52054"/>
+    /// </summary>
+    [Fact]
+    public void PreservesNoBomEncoding()
+    {
+        var testInstance = _testAssetsManager.CreateTestDirectory();
+        var tempFile = Path.Join(testInstance.Path, "test.cs");
+
+        // Create a file without BOM
+        var content = "#!/usr/bin/env dotnet run\nConsole.WriteLine();";
+        File.WriteAllText(tempFile, content, new UTF8Encoding(encoderShouldEmitUTF8Identifier: false));
+
+        // Load, modify, and save
+        var sourceFile = SourceFile.Load(tempFile);
+        var editor = FileBasedAppSourceEditor.Load(sourceFile);
+        editor.Add(new CSharpDirective.Package(default) { Name = "MyPackage", Version = "1.0.0" });
+        editor.SourceFile.Save();
+
+        // Verify no BOM was added
+        var bytes = File.ReadAllBytes(tempFile);
+        Assert.True(bytes is not [0xEF, 0xBB, 0xBF, ..],
+            "File should not have UTF-8 BOM");
+
+        // Verify shebang is still first
+        var savedContent = File.ReadAllText(tempFile);
+        Assert.StartsWith("#!/usr/bin/env dotnet run", savedContent);
+    }
+
+    /// <summary>
+    /// Verifies that files with UTF-8 BOM preserve it when saved.
+    /// <see href="https://github.com/dotnet/sdk/issues/52054"/>
+    /// </summary>
+    [Fact]
+    public void PreservesBomEncoding()
+    {
+        var testInstance = _testAssetsManager.CreateTestDirectory();
+        var tempFile = Path.Join(testInstance.Path, "test.cs");
+
+        // Create a file with BOM
+        var content = "Console.WriteLine();";
+        File.WriteAllText(tempFile, content, new UTF8Encoding(encoderShouldEmitUTF8Identifier: true));
+
+        // Load, modify, and save
+        var sourceFile = SourceFile.Load(tempFile);
+        var editor = FileBasedAppSourceEditor.Load(sourceFile);
+        editor.Add(new CSharpDirective.Package(default) { Name = "MyPackage", Version = "1.0.0" });
+        editor.SourceFile.Save();
+
+        // Verify BOM is still present
+        var bytes = File.ReadAllBytes(tempFile);
+        Assert.True(bytes is [0xEF, 0xBB, 0xBF, ..],
+            "File should have UTF-8 BOM");
+    }
+
+    /// <summary>
+    /// Verifies that files with non-UTF-8 encodings (like UTF-16) preserve their encoding when saved.
+    /// <see href="https://github.com/dotnet/sdk/issues/52054"/>
+    /// </summary>
+    [Fact]
+    public void PreservesNonUtf8Encoding()
+    {
+        var testInstance = _testAssetsManager.CreateTestDirectory();
+        var tempFile = Path.Join(testInstance.Path, "test.cs");
+
+        // Create a file with UTF-16 encoding (includes BOM by default)
+        var content = "Console.WriteLine(\"UTF-16 test\");";
+        File.WriteAllText(tempFile, content, Encoding.Unicode);
+
+        // Load, modify, and save
+        var sourceFile = SourceFile.Load(tempFile);
+        var editor = FileBasedAppSourceEditor.Load(sourceFile);
+        editor.Add(new CSharpDirective.Package(default) { Name = "MyPackage", Version = "1.0.0" });
+        editor.SourceFile.Save();
+
+        // Verify UTF-16 BOM is still present (0xFF 0xFE for UTF-16 LE)
+        var bytes = File.ReadAllBytes(tempFile);
+        Assert.True(bytes is [0xFF, 0xFE, ..],
+            "File should have UTF-16 LE BOM");
+
+        // Verify content is still readable as UTF-16
+        var savedContent = File.ReadAllText(tempFile, Encoding.Unicode);
+        Assert.Contains("#:package MyPackage@1.0.0", savedContent);
+        Assert.Contains("Console.WriteLine", savedContent);
+    }
+
     private void Verify(
         string input,
         params ReadOnlySpan<(Action<FileBasedAppSourceEditor> action, string expectedOutput)> verify)