diff --git a/src/Console/Command/Extract.php b/src/Console/Command/Extract.php
index 9596a0782..4ead856d3 100644
--- a/src/Console/Command/Extract.php
+++ b/src/Console/Command/Extract.php
@@ -38,6 +38,7 @@
  */
 final class Extract implements Command
 {
+    public const STUB_PATH = '.phar/stub.php';
     public const PHAR_META_PATH = '.phar_meta.json';
 
     private const PHAR_ARG = 'phar';
@@ -151,6 +152,7 @@ private static function dumpPhar(string $file, string $tmpDir): string
         $pubKey = $file.'.pubkey';
         $pubKeyContent = null;
         $tmpPubKey = $tmpFile.'.pubkey';
+        $stub = $tmpDir.DIRECTORY_SEPARATOR.self::STUB_PATH;
 
         try {
             FS::copy($file, $tmpFile, true);
@@ -164,6 +166,7 @@ private static function dumpPhar(string $file, string $tmpDir): string
             $pharMeta = PharMeta::fromPhar($phar, $pubKeyContent);
 
             $phar->extractTo($tmpDir);
+            FS::dumpFile($stub, $phar->getStub());
         } catch (Throwable $throwable) {
             FS::remove([$tmpFile, $tmpPubKey]);
 
diff --git a/src/Phar/Differ/ChecksumDiffer.php b/src/Phar/Differ/ChecksumDiffer.php
index 87cd060bd..7fdd40fdd 100644
--- a/src/Phar/Differ/ChecksumDiffer.php
+++ b/src/Phar/Differ/ChecksumDiffer.php
@@ -18,6 +18,7 @@
 use KevinGH\Box\Phar\PharInfo;
 use UnexpectedValueException;
 use ValueError;
+use function hash;
 use function implode;
 
 final class ChecksumDiffer implements Differ
@@ -110,6 +111,11 @@ private static function getFileHashesByRelativePathname(
         $hashFiles = [];
 
         try {
+            $hashFiles[$pharInfo->getStubPath()] = hash(
+                $algorithm,
+                $pharInfo->getStubContent(),
+            );
+
             foreach ($pharInfo->getFiles() as $file) {
                 $hashFiles[$file->getRelativePathname()] = hash_file(
                     $algorithm,
diff --git a/src/Phar/PharInfo.php b/src/Phar/PharInfo.php
index 58a7657fa..d3023e75d 100644
--- a/src/Phar/PharInfo.php
+++ b/src/Phar/PharInfo.php
@@ -247,6 +247,11 @@ public function getSignature(): ?array
         return $this->meta->signature;
     }
 
+    public function getStubPath(): string
+    {
+        return Extract::STUB_PATH;
+    }
+
     public function getStubContent(): ?string
     {
         return $this->meta->stub;
@@ -311,6 +316,7 @@ private static function loadDumpedPharFiles(string $tmp): array
                 Finder::create()
                     ->files()
                     ->ignoreDotFiles(false)
+                    ->exclude('.phar')
                     ->in($tmp),
             ),
         );
diff --git a/tests/Console/Command/DiffTest.php b/tests/Console/Command/DiffTest.php
index c5e759353..89e0ed992 100644
--- a/tests/Console/Command/DiffTest.php
+++ b/tests/Console/Command/DiffTest.php
@@ -578,7 +578,60 @@ public static function gitDiffPharsProvider(): iterable
 
     public static function GNUDiffPharsProvider(): iterable
     {
-        yield from self::commonDiffPharsProvider(DiffMode::GNU);
+        foreach (self::commonDiffPharsProvider(DiffMode::GNU) as $label => $set) {
+            yield $label => 'different data; same content' === $label
+                ? [
+                    self::FIXTURES_DIR.'/simple-phar-bar.phar',
+                    self::FIXTURES_DIR.'/simple-phar-bar-compressed.phar',
+                    sprintf(
+                        <<<'OUTPUT'
+
+                             // Comparing the two archives...
+
+                            Archive: simple-phar-bar.phar
+                            Archive Compression: None
+                            Files Compression: None
+                            Signature: SHA-1
+                            Signature Hash: 9ADC09F73909EDF14F8A4ABF9758B6FFAD1BBC51
+                            Metadata: None
+                            Timestamp: 1552839827 (2019-03-17T16:23:47+00:00)
+                            Contents: 1 file (6.64KB)
+
+                            Archive: simple-phar-bar-compressed.phar
+                            Archive Compression: None
+                            Files Compression: GZ
+                            Signature: SHA-1
+                            Signature Hash: 3A388D86C91C36659A043D52C2DEB64E8848DD1A
+                            Metadata: None
+                            Timestamp: 1552856416 (2019-03-17T21:00:16+00:00)
+                            Contents: 1 file (6.65KB)
+
+                            <diff-expected>--- PHAR A</diff-expected>
+                            <diff-actual>+++ PHAR B</diff-actual>
+                            @@ @@
+                             Archive Compression: None
+                            <diff-expected>-Files Compression: None</diff-expected>
+                            <diff-actual>+Files Compression: GZ</diff-actual>
+                             Signature: SHA-1
+                            <diff-expected>-Signature Hash: 9ADC09F73909EDF14F8A4ABF9758B6FFAD1BBC51</diff-expected>
+                            <diff-actual>+Signature Hash: 3A388D86C91C36659A043D52C2DEB64E8848DD1A</diff-actual>
+                             Metadata: None
+                            <diff-expected>-Timestamp: 1552839827 (2019-03-17T16:23:47+00:00)</diff-expected>
+                            <diff-expected>-Contents: 1 file (6.64KB)</diff-expected>
+                            <diff-actual>+Timestamp: 1552856416 (2019-03-17T21:00:16+00:00)</diff-actual>
+                            <diff-actual>+Contents: 1 file (6.65KB)</diff-actual>
+
+                             // Comparing the two archives contents (%s diff)...
+
+                            Common subdirectories: simple-phar-bar.phar/.phar and simple-phar-bar-compressed.phar/.phar
+
+                            OUTPUT,
+                        DiffMode::GNU->value,
+                    ),
+                    ExitCode::FAILURE,
+                ]
+                : $set;
+        }
 
         yield 'different files' => [
             self::FIXTURES_DIR.'/simple-phar-foo.phar',
@@ -620,6 +673,7 @@ public static function GNUDiffPharsProvider(): iterable
 
                  // Comparing the two archives contents (gnu diff)...
 
+                Common subdirectories: simple-phar-foo.phar/.phar and simple-phar-bar.phar/.phar
                 Only in simple-phar-bar.phar: bar.php
                 Only in simple-phar-foo.phar: foo.php
 
@@ -669,6 +723,7 @@ public static function GNUDiffPharsProvider(): iterable
 
                      // Comparing the two archives contents (gnu diff)...
 
+                    Common subdirectories: simple-phar-bar.phar/.phar and simple-phar-baz.phar/.phar
                     diff --exclude=.phar_meta.json simple-phar-bar.phar/bar.php simple-phar-baz.phar/bar.php
                     3c3
                     < echo "Hello world!";
@@ -714,6 +769,7 @@ public static function GNUDiffPharsProvider(): iterable
 
                      // Comparing the two archives contents (gnu diff)...
 
+                    Common subdirectories: simple-phar-bar.phar/.phar and simple-phar-baz.phar/.phar
                     diff '--exclude=.phar_meta.json' simple-phar-bar.phar/bar.php simple-phar-baz.phar/bar.php
                     3c3
                     < echo "Hello world!";
diff --git a/tests/Console/Command/ExtractTest.php b/tests/Console/Command/ExtractTest.php
index 484e609ac..d240c2a3e 100644
--- a/tests/Console/Command/ExtractTest.php
+++ b/tests/Console/Command/ExtractTest.php
@@ -99,6 +99,7 @@ private static function pharProvider(): iterable
         );
 
         $expectedSimplePharFiles = [
+            '.phar/stub.php' => $oldDefaultPharStub,
             '.hidden' => 'baz',
             'foo' => 'bar',
             '.phar_meta.json' => $pharMeta->toJson(),
@@ -118,6 +119,7 @@ private static function pharProvider(): iterable
             yield 'GZ compressed simple PHAR' => [
                 self::FIXTURES_DIR.'/gz-compressed-phar.phar',
                 [
+                    '.phar/stub.php' => $oldDefaultPharStub,
                     '.hidden' => 'baz',
                     'foo' => 'bar',
                     '.phar_meta.json' => (new PharMeta(
@@ -149,6 +151,7 @@ private static function pharProvider(): iterable
         yield 'sha512 signed PHAR' => [
             self::FIXTURES_DIR.'/sha512.phar',
             [
+                '.phar/stub.php' => $sha512Stub,
                 'index.php' => <<<'PHP'
                     <?php echo "Hello, world!\n";
 
@@ -177,6 +180,7 @@ private static function pharProvider(): iterable
         yield 'OpenSSL signed PHAR' => [
             self::FIXTURES_DIR.'/openssl.phar',
             [
+                '.phar/stub.php' => $sha512Stub,
                 'index.php' => <<<'PHP'
                     <?php echo "Hello, world!\n";