diff --git a/src/Building/UnixBuild.php b/src/Building/UnixBuild.php
index 384c547..6e7c994 100644
--- a/src/Building/UnixBuild.php
+++ b/src/Building/UnixBuild.php
@@ -45,8 +45,18 @@ public function __invoke(
             };
         }
 
+        $phpizePath ??= PhpizePath::guessFrom($targetPlatform->phpBinaryPath);
+
+        /**
+         * Call a cleanup first; most of the time, we expect to be changing a
+         * version (e.g. upgrade, downgrade), in which case the source is
+         * already clean anyway; however, sometimes we want to rebuild the
+         * current ext, so this will perform a clean first
+         */
+        $this->cleanup($phpizePath, $downloadedPackage, $output, $outputCallback);
+
         $this->phpize(
-            $phpizePath ?? PhpizePath::guessFrom($targetPlatform->phpBinaryPath),
+            $phpizePath,
             $downloadedPackage,
             $output,
             $outputCallback,
@@ -151,4 +161,40 @@ private function make(
             $outputCallback,
         );
     }
+
+    /** @param callable(SymfonyProcess::ERR|SymfonyProcess::OUT, string): void|null $outputCallback */
+    private function cleanup(
+        PhpizePath $phpize,
+        DownloadedPackage $downloadedPackage,
+        OutputInterface $output,
+        callable|null $outputCallback,
+    ): void {
+        /**
+         * A basic, but fallible check to see if we should clean first. This
+         * should work "most" of the time, unless someone has removed the
+         * configure script manually...
+         */
+        if (! file_exists($downloadedPackage->extractedSourcePath . '/configure')) {
+            if ($output->isVerbose()) {
+                $output->writeln('<comment>Skipping phpize --clean, configure does not exist</comment>');
+            }
+
+            return;
+        }
+
+        $phpizeCleanCommand = [$phpize->phpizeBinaryPath, '--clean'];
+
+        if ($output->isVerbose()) {
+            $output->writeln('<comment>Running phpize --clean step using: ' . implode(' ', $phpizeCleanCommand) . '</comment>');
+        }
+
+        Process::run(
+            $phpizeCleanCommand,
+            $downloadedPackage->extractedSourcePath,
+            self::PHPIZE_TIMEOUT_SECS,
+            $outputCallback,
+        );
+
+        $output->writeln('<info>Build files cleaned up.</info>');
+    }
 }
diff --git a/test/integration/Building/UnixBuildTest.php b/test/integration/Building/UnixBuildTest.php
index ce82c94..41bffb7 100644
--- a/test/integration/Building/UnixBuildTest.php
+++ b/test/integration/Building/UnixBuildTest.php
@@ -18,6 +18,7 @@
 use PHPUnit\Framework\Attributes\CoversClass;
 use PHPUnit\Framework\TestCase;
 use Symfony\Component\Console\Output\BufferedOutput;
+use Symfony\Component\Console\Output\OutputInterface;
 use Symfony\Component\Process\Process;
 
 use function dirname;
@@ -173,4 +174,88 @@ public function testUnixBuildCanBuildExtensionWithBuildPath(): void
         (new Process(['make', 'clean'], $downloadedPackage->extractedSourcePath))->mustRun();
         (new Process(['phpize', '--clean'], $downloadedPackage->extractedSourcePath))->mustRun();
     }
+
+    public function testCleanupDoesNotCleanWhenConfigureIsMissing(): void
+    {
+        if (Platform::isWindows()) {
+            self::markTestSkipped('Unix build test cannot be run on Windows');
+        }
+
+        (new Process(['phpize', '--clean'], self::TEST_EXTENSION_PATH))->mustRun();
+        self::assertFileDoesNotExist(self::TEST_EXTENSION_PATH . '/configure');
+
+        $output = new BufferedOutput();
+        $output->setVerbosity(OutputInterface::VERBOSITY_VERBOSE);
+
+        $downloadedPackage = DownloadedPackage::fromPackageAndExtractedPath(
+            new Package(
+                $this->createMock(CompletePackage::class),
+                ExtensionType::PhpModule,
+                ExtensionName::normaliseFromString('pie_test_ext'),
+                'pie_test_ext',
+                '0.1.0',
+                null,
+                [],
+                true,
+                true,
+                null,
+            ),
+            self::TEST_EXTENSION_PATH,
+        );
+
+        $unixBuilder = new UnixBuild();
+        $unixBuilder->__invoke(
+            $downloadedPackage,
+            TargetPlatform::fromPhpBinaryPath(PhpBinaryPath::fromCurrentProcess(), null),
+            ['--enable-pie_test_ext'],
+            $output,
+            null,
+        );
+
+        $outputString = $output->fetch();
+        self::assertStringContainsString('Skipping phpize --clean, configure does not exist', $outputString);
+        self::assertStringNotContainsString('Build files cleaned up', $outputString);
+    }
+
+    public function testVerboseOutputShowsCleanupMessages(): void
+    {
+        if (Platform::isWindows()) {
+            self::markTestSkipped('Unix build test cannot be run on Windows');
+        }
+
+        (new Process(['phpize'], self::TEST_EXTENSION_PATH))->mustRun();
+        self::assertFileExists(self::TEST_EXTENSION_PATH . '/configure');
+
+        $output = new BufferedOutput();
+        $output->setVerbosity(OutputInterface::VERBOSITY_VERBOSE);
+
+        $downloadedPackage = DownloadedPackage::fromPackageAndExtractedPath(
+            new Package(
+                $this->createMock(CompletePackage::class),
+                ExtensionType::PhpModule,
+                ExtensionName::normaliseFromString('pie_test_ext'),
+                'pie_test_ext',
+                '0.1.0',
+                null,
+                [ConfigureOption::fromComposerJsonDefinition(['name' => 'enable-pie_test_ext'])],
+                true,
+                true,
+                null,
+            ),
+            self::TEST_EXTENSION_PATH,
+        );
+
+        $unixBuilder = new UnixBuild();
+        $unixBuilder->__invoke(
+            $downloadedPackage,
+            TargetPlatform::fromPhpBinaryPath(PhpBinaryPath::fromCurrentProcess(), null),
+            ['--enable-pie_test_ext'],
+            $output,
+            null,
+        );
+
+        $outputString = $output->fetch();
+        self::assertStringContainsString('Running phpize --clean step', $outputString);
+        self::assertStringContainsString('Build files cleaned up', $outputString);
+    }
 }