diff --git a/src/Util/Path.php b/src/Util/Path.php
index 088d9121..c6508b4d 100644
--- a/src/Util/Path.php
+++ b/src/Util/Path.php
@@ -95,7 +95,7 @@ public static function isAnalysableFile(string $path, string $basePath): bool
      */
     public static function relativeTo(string $path, string $normalisedBasePath): string
     {
-        $normalisedPath = self::normalise($path, canonicalise: true);
+        $normalisedPath = self::normalise(self::resolve($path, $normalisedBasePath), canonicalise: true);
 
         if ($normalisedPath === $normalisedBasePath) {
             return '';
diff --git a/tests/Cli/StructArmedApplicationTest.php b/tests/Cli/StructArmedApplicationTest.php
index 96e900e4..0c39b0ee 100644
--- a/tests/Cli/StructArmedApplicationTest.php
+++ b/tests/Cli/StructArmedApplicationTest.php
@@ -19,9 +19,11 @@
 use PHPUnit\Framework\TestCase;
 
 use function bin2hex;
+use function chdir;
 use function file_exists;
 use function file_get_contents;
 use function file_put_contents;
+use function getcwd;
 use function glob;
 use function is_dir;
 use function json_decode;
@@ -1448,6 +1450,91 @@ public function testAnalyseCommandGeneratesBaseline(): void
         }
     }
 
+    /**
+     * A baseline entry stores its file relative to the base path. Running from
+     * a monorepo root that holds a file at the same relative path must not
+     * resolve the entry to that file instead.
+     */
+    public function testAnalyseCommandAppliesBaselineFromOtherWorkingDirectoryWithBasePathOption(): void
+    {
+        $rootPath    = (string) realpath($this->createTempDirectory());
+        $packagePath = $rootPath . '/packages/app';
+
+        mkdir($rootPath . '/src');
+        mkdir($packagePath . '/src', 0777, true);
+
+        $source = <<<'PHP'
+<?php
+
+namespace App;
+
+class Foo
+{
+}
+PHP;
+        file_put_contents($rootPath . '/src/Foo.php', $source);
+        file_put_contents($packagePath . '/src/Foo.php', $source);
+        file_put_contents($packagePath . '/structarmed.php', <<<'PHP'
+<?php
+
+declare(strict_types=1);
+
+use Boundwize\StructArmed\Architecture;
+use Boundwize\StructArmed\Rule\Rules\Class_\MustBeFinalRule;
+
+return Architecture::define()
+    ->layer('Source', 'src/')
+    ->rule('source.must_be_final', new MustBeFinalRule('Source'))
+    ->baseline('structarmed-baseline.php');
+PHP);
+
+        $originalWorkingDirectory = getcwd();
+        $this->assertNotFalse($originalWorkingDirectory);
+
+        try {
+            [$generateExitCode, $generateOutput] = $this->runApplication(
+                [
+                    'structarmed',
+                    'analyse',
+                    '--no-progress',
+                    '--no-cache',
+                    '--generate-baseline=structarmed-baseline.php',
+                ],
+                $packagePath
+            );
+
+            $this->assertSame(0, $generateExitCode, $generateOutput);
+            $this->assertStringContainsString(
+                "'file' => 'src/Foo.php'",
+                (string) file_get_contents($packagePath . '/structarmed-baseline.php')
+            );
+
+            chdir($rootPath);
+
+            [$exitCode, $output] = $this->runApplication(
+                [
+                    'structarmed',
+                    'analyse',
+                    '--basepath=packages/app',
+                    '--config=packages/app/structarmed.php',
+                    '--no-progress',
+                    '--no-cache',
+                ],
+                $rootPath
+            );
+
+            $this->assertSame(0, $exitCode, $output);
+            $this->assertStringContainsString('No violations found.', $output);
+        } finally {
+            chdir($originalWorkingDirectory);
+            $this->removeTempDirectory($packagePath);
+            unlink($rootPath . '/src/Foo.php');
+            rmdir($rootPath . '/src');
+            rmdir($rootPath . '/packages');
+            rmdir($rootPath);
+        }
+    }
+
     public function testAnalyseCommandGeneratesBaselineWithSeparateOptionValue(): void
     {
         $basePath = $this->createProjectDirectoryWithViolation();
diff --git a/tests/Util/PathTest.php b/tests/Util/PathTest.php
index 21926b7c..8090832c 100644
--- a/tests/Util/PathTest.php
+++ b/tests/Util/PathTest.php
@@ -92,6 +92,9 @@ public static function provideRelativeTo(): Iterator
         yield 'base itself' => ['/project', '/project', ''];
         yield 'sibling of base' => ['/shared/src/Foo.php', '/project', '../shared/src/Foo.php'];
         yield 'no common ancestor' => ['C:/other/Foo.php', '/project', 'C:/other/Foo.php'];
+        // resolved against the base path, never the working directory
+        yield 'relative to base' => ['src/Foo.php', '/project', 'src/Foo.php'];
+        yield 'empty is the base' => ['', '/project', ''];
     }
 
     #[DataProvider('provideRelativeTo')]