diff --git a/src/Command/BuildCommand.php b/src/Command/BuildCommand.php
index 8fd323dc..8f0b967f 100644
--- a/src/Command/BuildCommand.php
+++ b/src/Command/BuildCommand.php
@@ -54,6 +54,7 @@ public function configure(): void
     public function execute(InputInterface $input, OutputInterface $output): int
     {
         $targetPlatform = CommandHelper::determineTargetPlatformFromInputs($input, $this->io);
+        CommandHelper::assertExtensionPathIsConsistent($targetPlatform, $input, $this->io);
         try {
             $requestedNamesAndVersions = CommandHelper::requestedNameAndVersionPairs($input);
         } catch (InvalidPackageName $invalidPackageName) {
diff --git a/src/Command/CommandHelper.php b/src/Command/CommandHelper.php
index b54ae8bb..ecd6c39f 100644
--- a/src/Command/CommandHelper.php
+++ b/src/Command/CommandHelper.php
@@ -31,7 +31,9 @@
 use Php\Pie\Platform\TargetPhp\PhpBinaryPath;
 use Php\Pie\Platform\TargetPhp\PhpizePath;
 use Php\Pie\Platform\TargetPlatform;
+use Php\Pie\Util\Realpath;
 use Psr\Container\ContainerInterface;
+use RuntimeException;
 use Symfony\Component\Console\Command\Command;
 use Symfony\Component\Console\Input\InputArgument;
 use Symfony\Component\Console\Input\InputInterface;
@@ -313,6 +315,34 @@ public static function determineForceInstallingPackageVersion(InputInterface $in
         return $input->hasOption(self::OPTION_FORCE) && $input->getOption(self::OPTION_FORCE);
     }
 
+    public static function assertExtensionPathIsConsistent(TargetPlatform $targetPlatform, InputInterface $input, IOInterface $io): void
+    {
+        $phpConfigExtensionPath = $targetPlatform->phpBinaryPath->phpConfigExtensionPath();
+        $iniExtensionPath       = $targetPlatform->phpBinaryPath->extensionPath();
+
+        if ($phpConfigExtensionPath === null || Realpath::compare($phpConfigExtensionPath, $iniExtensionPath)) {
+            return;
+        }
+
+        $message = sprintf(
+            <<<'ERROR'
+            The php.ini `extension_dir` directive (%s) does not match `php-config --extension-dir` (%s). This means
+            that installs will likely fail (as the extension will be installed in one place, but PHP is looking in
+            another place).
+
+
+            ERROR,
+            $iniExtensionPath,
+            $phpConfigExtensionPath,
+        );
+
+        if (! self::determineForceInstallingPackageVersion($input)) {
+            throw new RuntimeException($message . 'Re-run with --force to attempt the install anyway.');
+        }
+
+        $io->writeError('<comment>Warning: ' . $message . 'Proceeding anyway because --force was used.</comment>');
+    }
+
     public static function noDev(InputInterface $input): bool
     {
         return $input->hasOption(self::OPTION_NO_DEV) && $input->getOption(self::OPTION_NO_DEV);
diff --git a/src/Command/InstallCommand.php b/src/Command/InstallCommand.php
index c978c0fe..d75bb2dc 100644
--- a/src/Command/InstallCommand.php
+++ b/src/Command/InstallCommand.php
@@ -92,6 +92,7 @@ public function execute(InputInterface $input, OutputInterface $output): int
         }
 
         $targetPlatform = CommandHelper::determineTargetPlatformFromInputs($input, $this->io);
+        CommandHelper::assertExtensionPathIsConsistent($targetPlatform, $input, $this->io);
         try {
             $requestedNamesAndVersions = CommandHelper::requestedNameAndVersionPairs($input);
         } catch (InvalidPackageName $invalidPackageName) {
diff --git a/src/Command/InstallExtensionsForProjectCommand.php b/src/Command/InstallExtensionsForProjectCommand.php
index da46af88..6c2bf9ad 100644
--- a/src/Command/InstallExtensionsForProjectCommand.php
+++ b/src/Command/InstallExtensionsForProjectCommand.php
@@ -109,6 +109,7 @@ private function handlePhpProject(InputInterface $input, RootPackageInterface $r
     {
         $extensionToPackageSelections = CommandHelper::determineExtensionToPackageSelections($input);
         $targetPlatform               = CommandHelper::determineTargetPlatformFromInputs($input, $this->io);
+        CommandHelper::assertExtensionPathIsConsistent($targetPlatform, $input, $this->io);
 
         $allowNonInteractive = $input->hasOption(CommandHelper::OPTION_ALLOW_NON_INTERACTIVE_PROJECT_INSTALL) && $input->getOption(CommandHelper::OPTION_ALLOW_NON_INTERACTIVE_PROJECT_INSTALL);
         if ($allowNonInteractive) {
diff --git a/src/Command/UpgradeCommand.php b/src/Command/UpgradeCommand.php
index d644d4a1..f69cf87e 100644
--- a/src/Command/UpgradeCommand.php
+++ b/src/Command/UpgradeCommand.php
@@ -55,6 +55,7 @@ public function execute(InputInterface $input, OutputInterface $output): int
         }
 
         $targetPlatform = CommandHelper::determineTargetPlatformFromInputs($input, $this->io);
+        CommandHelper::assertExtensionPathIsConsistent($targetPlatform, $input, $this->io);
 
         $forceInstallPackageVersion = CommandHelper::determineForceInstallingPackageVersion($input);
         CommandHelper::applyNoCacheOptionIfSet($input, $this->io);
diff --git a/src/Platform/TargetPhp/PhpBinaryPath.php b/src/Platform/TargetPhp/PhpBinaryPath.php
index 7f001a4f..cd2f78d0 100644
--- a/src/Platform/TargetPhp/PhpBinaryPath.php
+++ b/src/Platform/TargetPhp/PhpBinaryPath.php
@@ -154,6 +154,18 @@ public function extensionPath(string|null $prefixInstallRoot = null): string
         throw ExtensionPathProblem::new($this, $extensionPath);
     }
 
+    /** @return non-empty-string|null */
+    public function phpConfigExtensionPath(): string|null
+    {
+        if ($this->phpConfigPath === null) {
+            return null;
+        }
+
+        $extensionDir = self::cleanWarningAndDeprecationsFromOutput(Process::run([$this->phpConfigPath, '--extension-dir']));
+
+        return $extensionDir !== '' ? $extensionDir : null;
+    }
+
     public function assertExtensionIsLoadedInRuntime(ExtensionName $extension, IOInterface|null $io = null): void
     {
         if (! in_array(strtolower($extension->name()), array_map('strtolower', array_keys($this->extensions())))) {
diff --git a/src/Util/Realpath.php b/src/Util/Realpath.php
new file mode 100644
index 00000000..ec30a090
--- /dev/null
+++ b/src/Util/Realpath.php
@@ -0,0 +1,15 @@
+<?php
+
+declare(strict_types=1);
+
+namespace Php\Pie\Util;
+
+use function Safe\realpath;
+
+final class Realpath
+{
+    public static function compare(string $path1, string $path2): bool
+    {
+        return realpath($path1) === realpath($path2);
+    }
+}
diff --git a/test/unit/Command/CommandHelperTest.php b/test/unit/Command/CommandHelperTest.php
index eeb3c985..f0a87101 100644
--- a/test/unit/Command/CommandHelperTest.php
+++ b/test/unit/Command/CommandHelperTest.php
@@ -24,11 +24,17 @@
 use Php\Pie\DependencyResolver\ResolvedPackageRequest;
 use Php\Pie\DependencyResolver\UnableToResolveRequirement;
 use Php\Pie\Downloading\DownloadUrlMethod;
+use Php\Pie\Platform\Architecture;
+use Php\Pie\Platform\OperatingSystem;
+use Php\Pie\Platform\OperatingSystemFamily;
+use Php\Pie\Platform\TargetPhp\PhpBinaryPath;
 use Php\Pie\Platform\TargetPlatform;
+use Php\Pie\Platform\ThreadSafetyMode;
 use PHPUnit\Framework\Attributes\CoversClass;
 use PHPUnit\Framework\Attributes\DataProvider;
 use PHPUnit\Framework\Attributes\RequiresOperatingSystemFamily;
 use PHPUnit\Framework\TestCase;
+use RuntimeException;
 use Symfony\Component\Console\Command\Command;
 use Symfony\Component\Console\Input\ArrayInput;
 use Symfony\Component\Console\Input\InputDefinition;
@@ -37,8 +43,14 @@
 
 use function array_combine;
 use function array_map;
+use function Safe\mkdir;
+use function Safe\symlink;
 use function str_replace;
+use function sys_get_temp_dir;
 use function trim;
+use function uniqid;
+
+use const DIRECTORY_SEPARATOR;
 
 #[CoversClass(CommandHelper::class)]
 final class CommandHelperTest extends TestCase
@@ -376,6 +388,118 @@ public function testDetermineSuppressedDownloadUrlMethodsThrowsForInvalidValue()
         CommandHelper::determineSuppressedDownloadUrlMethods($input);
     }
 
+    private function targetPlatformWithExtensionPaths(string|null $phpConfigExtensionPath, string $iniExtensionPath): TargetPlatform
+    {
+        $phpBinary = $this->createMock(PhpBinaryPath::class);
+        $phpBinary->method('phpConfigExtensionPath')->willReturn($phpConfigExtensionPath);
+        $phpBinary->method('extensionPath')->willReturn($iniExtensionPath);
+
+        return new TargetPlatform(
+            OperatingSystem::NonWindows,
+            OperatingSystemFamily::Linux,
+            $phpBinary,
+            Architecture::x86_64,
+            ThreadSafetyMode::NonThreadSafe,
+            1,
+            null,
+            null,
+        );
+    }
+
+    /** @return non-empty-string */
+    private function realTempDir(): string
+    {
+        $dir = sys_get_temp_dir() . DIRECTORY_SEPARATOR . uniqid('pie-test-extension-dir-', true);
+        mkdir($dir, 0777, true);
+
+        return $dir;
+    }
+
+    public function testAssertExtensionPathDoesNothingWhenPhpConfigNotUsed(): void
+    {
+        $targetPlatform = $this->targetPlatformWithExtensionPaths(null, $this->realTempDir());
+        $io             = new BufferIO();
+
+        CommandHelper::assertExtensionPathIsConsistent($targetPlatform, new ArrayInput([]), $io);
+
+        self::assertSame('', $io->getOutput());
+    }
+
+    public function testAssertExtensionPathDoesNothingWhenPathsMatch(): void
+    {
+        $dir            = $this->realTempDir();
+        $targetPlatform = $this->targetPlatformWithExtensionPaths($dir, $dir);
+        $io             = new BufferIO();
+
+        CommandHelper::assertExtensionPathIsConsistent($targetPlatform, new ArrayInput([]), $io);
+
+        self::assertSame('', $io->getOutput());
+    }
+
+    public function testAssertExtensionPathDoesNothingWhenPathsAreSymlinkedToTheSameRealPath(): void
+    {
+        if (Platform::isWindows()) {
+            self::markTestSkipped('Skipping for Windows as ineffective');
+        }
+
+        $realDir = $this->realTempDir();
+
+        $symlinkPath = sys_get_temp_dir() . DIRECTORY_SEPARATOR . uniqid('pie-test-extension-dir-symlink-', true);
+        symlink($realDir, $symlinkPath);
+
+        $targetPlatform = $this->targetPlatformWithExtensionPaths($symlinkPath, $realDir);
+        $io             = new BufferIO();
+
+        CommandHelper::assertExtensionPathIsConsistent($targetPlatform, new ArrayInput([]), $io);
+
+        self::assertSame('', $io->getOutput());
+    }
+
+    public function testAssertExtensionPathThrowsWhenPathsMatch(): void
+    {
+        $phpConfigExtensionPath = $this->realTempDir();
+        $iniExtensionPath       = $this->realTempDir();
+        $targetPlatform         = $this->targetPlatformWithExtensionPaths($phpConfigExtensionPath, $iniExtensionPath);
+
+        $this->expectException(RuntimeException::class);
+        $this->expectExceptionMessage(<<<EXCEPTION
+            The php.ini `extension_dir` directive ($iniExtensionPath) does not match `php-config --extension-dir` ($phpConfigExtensionPath). This means
+            that installs will likely fail (as the extension will be installed in one place, but PHP is looking in
+            another place).
+
+            Re-run with --force to attempt the install anyway.
+            EXCEPTION);
+
+        CommandHelper::assertExtensionPathIsConsistent($targetPlatform, new ArrayInput([]), new BufferIO());
+    }
+
+    public function testAssertExtensionPathWarnsWhenPathsMatchButLukeUsesTheForce(): void
+    {
+        $phpConfigExtensionPath = $this->realTempDir();
+        $iniExtensionPath       = $this->realTempDir();
+        $targetPlatform         = $this->targetPlatformWithExtensionPaths($phpConfigExtensionPath, $iniExtensionPath);
+
+        $command = new Command();
+        CommandHelper::configureDownloadBuildInstallOptions($command);
+        $input = new ArrayInput(['--force' => true]);
+        CommandHelper::validateInput($input, $command);
+
+        $io = new BufferIO();
+
+        CommandHelper::assertExtensionPathIsConsistent($targetPlatform, $input, $io);
+
+        self::assertStringContainsString(
+            <<<WARNING
+            Warning: The php.ini `extension_dir` directive ($iniExtensionPath) does not match `php-config --extension-dir` ($phpConfigExtensionPath). This means
+            that installs will likely fail (as the extension will be installed in one place, but PHP is looking in
+            another place).
+
+            Proceeding anyway because --force was used.
+            WARNING,
+            $io->getOutput(),
+        );
+    }
+
     public function testListRepositories(): void
     {
         $io = new BufferIO();
diff --git a/test/unit/Platform/TargetPhp/PhpBinaryPathTest.php b/test/unit/Platform/TargetPhp/PhpBinaryPathTest.php
index 95275522..096918b0 100644
--- a/test/unit/Platform/TargetPhp/PhpBinaryPathTest.php
+++ b/test/unit/Platform/TargetPhp/PhpBinaryPathTest.php
@@ -194,6 +194,21 @@ public function testFromPhpConfigExecutable(string $phpConfigPath, string $expec
         );
 
         self::assertSame($phpConfigPath, $phpBinary->phpConfigPath());
+
+        self::assertSame(
+            Process::run([$phpConfigPath, '--extension-dir']),
+            $phpBinary->phpConfigExtensionPath(),
+        );
+    }
+
+    public function testPhpConfigExtensionPathIsNullWhenPhpConfigIsNotPresent(): void
+    {
+        $phpExecutable = trim((string) (new PhpExecutableFinder())->find());
+        assert($phpExecutable !== '');
+
+        $phpBinary = PhpBinaryPath::fromPhpBinaryPath($phpExecutable);
+
+        self::assertNull($phpBinary->phpConfigExtensionPath());
     }
 
     public function testExtensions(): void
diff --git a/test/unit/Util/RealpathTest.php b/test/unit/Util/RealpathTest.php
new file mode 100644
index 00000000..c459e5a2
--- /dev/null
+++ b/test/unit/Util/RealpathTest.php
@@ -0,0 +1,63 @@
+<?php
+
+declare(strict_types=1);
+
+namespace Php\PieUnitTest\Util;
+
+use Composer\Util\Platform;
+use Php\Pie\Util\Realpath;
+use PHPUnit\Framework\Attributes\CoversClass;
+use PHPUnit\Framework\TestCase;
+
+use function Safe\mkdir;
+use function Safe\symlink;
+use function sys_get_temp_dir;
+use function uniqid;
+
+use const DIRECTORY_SEPARATOR;
+
+#[CoversClass(Realpath::class)]
+final class RealpathTest extends TestCase
+{
+    /** @return non-empty-string */
+    private function realTempDir(): string
+    {
+        $dir = sys_get_temp_dir() . DIRECTORY_SEPARATOR . uniqid('pie-test-realpath-', true);
+        mkdir($dir, 0777, true);
+
+        return $dir;
+    }
+
+    public function testSamePathIsEqual(): void
+    {
+        $dir = $this->realTempDir();
+
+        self::assertTrue(Realpath::compare($dir, $dir));
+    }
+
+    public function testDifferentPathsAreNotEqual(): void
+    {
+        self::assertFalse(Realpath::compare($this->realTempDir(), $this->realTempDir()));
+    }
+
+    public function testSymlinkedPathIsEqualToItsRealTarget(): void
+    {
+        if (Platform::isWindows()) {
+            self::markTestSkipped('Skipping for Windows as ineffective');
+        }
+
+        $realDir = $this->realTempDir();
+
+        $symlinkPath = sys_get_temp_dir() . DIRECTORY_SEPARATOR . uniqid('pie-test-realpath-symlink-', true);
+        symlink($realDir, $symlinkPath);
+
+        self::assertTrue(Realpath::compare($symlinkPath, $realDir));
+    }
+
+    public function testTrailingDirectorySeparatorIsNormalised(): void
+    {
+        $dir = $this->realTempDir();
+
+        self::assertTrue(Realpath::compare($dir, $dir . DIRECTORY_SEPARATOR));
+    }
+}