diff --git a/docs/assets/no-violation.svg b/docs/assets/no-violation.svg
index be47332..f5b65d6 100644
--- a/docs/assets/no-violation.svg
+++ b/docs/assets/no-violation.svg
@@ -14,7 +14,7 @@
         <text x="0" y="0" class="text"><tspan class="prompt">➜  </tspan><tspan class="dir">prj-ddd </tspan><tspan class="cmd">vendor/bin/structarmed analyze</tspan></text>
 
         <!-- Line 3: Title and Version -->
-        <text x="0" y="35" class="text header">StructArmed <tspan class="version">0.14.5</tspan> — Architecture Enforcement</text>
+        <text x="0" y="35" class="text header">StructArmed <tspan class="version">0.14.6</tspan> — Architecture Enforcement</text>
 
         <!-- Line 4: Separator (Reduced length) -->
         <text x="0" y="49" class="text">===============================================</text>
diff --git a/docs/assets/structarmed-showoff.svg b/docs/assets/structarmed-showoff.svg
index 43017dc..0bf7332 100644
--- a/docs/assets/structarmed-showoff.svg
+++ b/docs/assets/structarmed-showoff.svg
@@ -15,7 +15,7 @@
         <text x="0" y="0" class="text"><tspan class="prompt">➜  </tspan><tspan class="dir">prj-ddd </tspan><tspan class="cmd">vendor/bin/structarmed analyze</tspan></text>
 
         <!-- Line 3: Title and Version -->
-        <text x="0" y="35" class="text header">StructArmed <tspan class="version">0.14.5</tspan> — Architecture Enforcement</text>
+        <text x="0" y="35" class="text header">StructArmed <tspan class="version">0.14.6</tspan> — Architecture Enforcement</text>
 
         <!-- Line 4: Separator -->
         <text x="0" y="49" class="text">===============================================</text>
diff --git a/src/Cli/AnalyseCommand.php b/src/Cli/AnalyseCommand.php
index c56ba08..4554c14 100644
--- a/src/Cli/AnalyseCommand.php
+++ b/src/Cli/AnalyseCommand.php
@@ -183,69 +183,54 @@ public function run(array $arguments, string $basePath): int
             $analysisResultCache->store($cacheKey, $metadata, $ruleViolationCollection);
         }
 
-        $elapsed  = microtime(true) - $start;
-        $baseline = new Baseline();
+        $elapsed                           = microtime(true) - $start;
+        $baseline                          = new Baseline();
+        $unfilteredRuleViolationCollection = $ruleViolationCollection;
+        $shouldGenerateBaseline            = isset($options['generate-baseline']);
+        $fixedCount                        = 0;
 
-        if (isset($options['generate-baseline'])) {
+        if (isset($options['fix'])) {
             try {
-                $baseline->generate($ruleViolationCollection, $options['generate-baseline'], $basePath);
+                $ruleViolationCollection = $this->resolveRuleViolationCollection(
+                    $unfilteredRuleViolationCollection,
+                    $architecture,
+                    $basePath,
+                    $shouldGenerateBaseline
+                );
             } catch (RuntimeException $runtimeException) {
                 echo 'Error: ' . $runtimeException->getMessage() . PHP_EOL;
 
                 return 1;
             }
 
-            echo sprintf(
-                "Generated baseline [%s] with %d violation(s).\n",
-                $options['generate-baseline'],
-                $ruleViolationCollection->count()
-            );
-
-            return 0;
-        }
-
-        try {
-            $ruleViolationCollection = (new BaselineFilter())->apply(
-                $ruleViolationCollection,
-                $architecture,
-                $basePath
-            );
-        } catch (RuntimeException $runtimeException) {
-            echo 'Error: ' . $runtimeException->getMessage() . PHP_EOL;
-
-            return 1;
-        }
-
-        $fixedCount = 0;
-
-        if (isset($options['fix'])) {
             $fixedCount = $this->fixViolations($architecture, $ruleViolationCollection);
 
             if ($fixedCount > 0) {
                 $analysisResultCache->clear();
 
-                $files                   = $analyser->filesForAnalysis($architecture, $scanPaths);
-                $metadata                = $analysisCacheMetadataFactory->metadata(
+                $files                             = $analyser->filesForAnalysis($architecture, $scanPaths);
+                $metadata                          = $analysisCacheMetadataFactory->metadata(
                     $basePath,
                     $configFile,
                     $scanPaths,
                     $files
                 );
-                $cacheKey                = $analysisCacheMetadataFactory->key($metadata);
-                $ruleViolationCollection = $analyser->analyse(
+                $cacheKey                          = $analysisCacheMetadataFactory->key($metadata);
+                $unfilteredRuleViolationCollection = $analyser->analyse(
                     $architecture,
                     $scanPaths,
                     null,
                     $analyserOptions,
                     $files
                 );
-                $analysisResultCache->store($cacheKey, $metadata, $ruleViolationCollection);
+                $analysisResultCache->store($cacheKey, $metadata, $unfilteredRuleViolationCollection);
 
                 try {
-                    $ruleViolationCollection = (new BaselineFilter())->apply(
-                        $ruleViolationCollection,
+                    $ruleViolationCollection = $this->resolveRuleViolationCollection(
+                        $unfilteredRuleViolationCollection,
                         $architecture,
-                        $basePath
+                        $basePath,
+                        $shouldGenerateBaseline
                     );
                 } catch (RuntimeException $runtimeException) {
                     echo 'Error: ' . $runtimeException->getMessage() . PHP_EOL;
@@ -255,6 +240,41 @@ public function run(array $arguments, string $basePath): int
 
                 $elapsed = microtime(true) - $start;
             }
+        } else {
+            try {
+                $ruleViolationCollection = $this->resolveRuleViolationCollection(
+                    $unfilteredRuleViolationCollection,
+                    $architecture,
+                    $basePath,
+                    $shouldGenerateBaseline
+                );
+            } catch (RuntimeException $runtimeException) {
+                echo 'Error: ' . $runtimeException->getMessage() . PHP_EOL;
+
+                return 1;
+            }
+        }
+
+        if ($reportType === 'console' && $fixedCount > 0) {
+            echo PHP_EOL . $this->fixedViolationMessage($fixedCount) . PHP_EOL;
+        }
+
+        if ($shouldGenerateBaseline) {
+            try {
+                $baseline->generate($unfilteredRuleViolationCollection, $options['generate-baseline'], $basePath);
+            } catch (RuntimeException $runtimeException) {
+                echo 'Error: ' . $runtimeException->getMessage() . PHP_EOL;
+
+                return 1;
+            }
+
+            echo sprintf(
+                "Generated baseline [%s] with %d violation(s).\n",
+                $options['generate-baseline'],
+                $unfilteredRuleViolationCollection->count()
+            );
+
+            return 0;
         }
 
         $report = match ($reportType) {
@@ -262,15 +282,24 @@ public function run(array $arguments, string $basePath): int
             default => (new ConsoleReport())->render($ruleViolationCollection, $elapsed),
         };
 
-        if ($reportType === 'console' && $fixedCount > 0) {
-            echo PHP_EOL . $this->fixedViolationMessage($fixedCount) . PHP_EOL;
-        }
-
         echo $report;
 
         return $ruleViolationCollection->hasViolations() ? 1 : 0;
     }
 
+    private function resolveRuleViolationCollection(
+        RuleViolationCollection $unfilteredRuleViolationCollection,
+        Architecture $architecture,
+        string $basePath,
+        bool $shouldGenerateBaseline
+    ): RuleViolationCollection {
+        if ($shouldGenerateBaseline) {
+            return $unfilteredRuleViolationCollection;
+        }
+
+        return (new BaselineFilter())->apply($unfilteredRuleViolationCollection, $architecture, $basePath);
+    }
+
     private function fixViolations(Architecture $architecture, RuleViolationCollection $ruleViolationCollection): int
     {
         $rules      = $architecture->getRules();
diff --git a/tests/Cli/AnalyseCommandTest.php b/tests/Cli/AnalyseCommandTest.php
new file mode 100644
index 0000000..738a218
--- /dev/null
+++ b/tests/Cli/AnalyseCommandTest.php
@@ -0,0 +1,35 @@
+<?php
+
+declare(strict_types=1);
+
+namespace Boundwize\StructArmed\Tests\Cli;
+
+use Boundwize\StructArmed\Cli\AnalyseCommand;
+use PHPUnit\Framework\Attributes\CoversClass;
+use PHPUnit\Framework\Attributes\DataProvider;
+use PHPUnit\Framework\TestCase;
+use ReflectionMethod;
+
+#[CoversClass(AnalyseCommand::class)]
+final class AnalyseCommandTest extends TestCase
+{
+    /**
+     * @return iterable<string, array{int, string}>
+     */
+    public static function fixedViolationMessageProvider(): iterable
+    {
+        yield 'singular' => [1, '1 violation has been fixed.'];
+        yield 'plural'   => [2, '2 violations have been fixed.'];
+    }
+
+    #[DataProvider('fixedViolationMessageProvider')]
+    public function testFormatsFixedViolationMessage(int $fixedCount, string $expectedMessage): void
+    {
+        $reflectionMethod = new ReflectionMethod(AnalyseCommand::class, 'fixedViolationMessage');
+
+        $message = $reflectionMethod->invoke(new AnalyseCommand(), $fixedCount);
+
+        $this->assertIsString($message);
+        $this->assertStringContainsString($expectedMessage, $message);
+    }
+}
diff --git a/tests/Cli/StructArmedApplicationTest.php b/tests/Cli/StructArmedApplicationTest.php
index 11388e4..51e5ddb 100644
--- a/tests/Cli/StructArmedApplicationTest.php
+++ b/tests/Cli/StructArmedApplicationTest.php
@@ -636,6 +636,178 @@ public function testAnalyseCommandGeneratesBaselineWithSeparateOptionValue(): vo
         }
     }
 
+    public function testAnalyseCommandFixesViolationsBeforeGeneratingBaseline(): void
+    {
+        $basePath = $this->createProjectDirectoryWithImplicitMethodVisibilityViolation();
+
+        try {
+            [$exitCode, $output] = $this->runApplication(
+                [
+                    'structarmed',
+                    'analyse',
+                    '--config=' . $basePath . '/structarmed.php',
+                    '--fix',
+                    '--no-progress',
+                    '--generate-baseline=structarmed-baseline.php',
+                ],
+                $basePath
+            );
+
+            $this->assertSame(0, $exitCode, $output);
+            $this->assertStringContainsString(
+                'Generated baseline [structarmed-baseline.php] with 0 violation(s).',
+                $output
+            );
+            $this->assertStringContainsString(
+                '    public function handle(): void',
+                (string) file_get_contents($basePath . '/src/Foo.php')
+            );
+            $this->assertSame(
+                <<<'PHP'
+<?php
+
+declare(strict_types=1);
+
+return [];
+
+PHP,
+                file_get_contents($basePath . '/structarmed-baseline.php')
+            );
+        } finally {
+            $this->removeTempDirectory($basePath);
+        }
+    }
+
+    public function testAnalyseCommandReportsFixedCountWhenGeneratingBaselineAfterFix(): void
+    {
+        $basePath = $this->createProjectDirectoryWithImplicitMethodVisibilityViolation();
+
+        try {
+            [$exitCode, $output] = $this->runApplication(
+                [
+                    'structarmed',
+                    'analyse',
+                    '--config=' . $basePath . '/structarmed.php',
+                    '--fix',
+                    '--no-progress',
+                    '--generate-baseline=structarmed-baseline.php',
+                ],
+                $basePath
+            );
+
+            $this->assertSame(0, $exitCode, $output);
+            $this->assertStringContainsString(
+                '1 violation has been fixed.',
+                $this->withoutAnsi($output)
+            );
+            $this->assertStringContainsString(
+                'Generated baseline [structarmed-baseline.php] with 0 violation(s).',
+                $output
+            );
+        } finally {
+            $this->removeTempDirectory($basePath);
+        }
+    }
+
+    public function testAnalyseCommandCanFixAndGenerateMissingConfiguredBaseline(): void
+    {
+        $basePath = $this->createProjectDirectoryWithImplicitMethodVisibilityViolation();
+
+        try {
+            file_put_contents($basePath . '/structarmed.php', <<<'PHP'
+<?php
+
+declare(strict_types=1);
+
+use Boundwize\StructArmed\Architecture;
+use Boundwize\StructArmed\Rule\Rules\Class_\MustDeclareMethodVisibilityRule;
+
+return Architecture::define()
+    ->baseline('structarmed-baseline.php')
+    ->layer('Source', 'src/')
+    ->rule('source.must_declare_method_visibility', new MustDeclareMethodVisibilityRule('Source'));
+PHP);
+
+            [$exitCode, $output] = $this->runApplication(
+                [
+                    'structarmed',
+                    'analyse',
+                    '--config=' . $basePath . '/structarmed.php',
+                    '--fix',
+                    '--no-progress',
+                    '--generate-baseline=structarmed-baseline.php',
+                ],
+                $basePath
+            );
+
+            $this->assertSame(0, $exitCode, $output);
+            $this->assertStringContainsString(
+                'Generated baseline [structarmed-baseline.php] with 0 violation(s).',
+                $output
+            );
+            $this->assertStringContainsString(
+                '    public function handle(): void',
+                (string) file_get_contents($basePath . '/src/Foo.php')
+            );
+            $this->assertFileExists($basePath . '/structarmed-baseline.php');
+        } finally {
+            $this->removeTempDirectory($basePath);
+        }
+    }
+
+    public function testAnalyseCommandGeneratesBaselineFromRemainingViolationsAfterFix(): void
+    {
+        $basePath = $this->createProjectDirectoryWithImplicitMethodVisibilityViolation();
+
+        try {
+            file_put_contents($basePath . '/structarmed.php', <<<'PHP'
+<?php
+
+declare(strict_types=1);
+
+use Boundwize\StructArmed\Architecture;
+use Boundwize\StructArmed\Rule\Rules\Class_\ClassNameMustHaveSuffixRule;
+use Boundwize\StructArmed\Rule\Rules\Class_\MustDeclareMethodVisibilityRule;
+
+return Architecture::define()
+    ->layer('Source', 'src/')
+    ->rule('source.must_declare_method_visibility', new MustDeclareMethodVisibilityRule('Source'))
+    ->rule('source.class_name_must_have_suffix', new ClassNameMustHaveSuffixRule('Source', 'Service'));
+PHP);
+
+            [$exitCode, $output] = $this->runApplication(
+                [
+                    'structarmed',
+                    'analyse',
+                    '--config=' . $basePath . '/structarmed.php',
+                    '--fix',
+                    '--no-progress',
+                    '--generate-baseline=structarmed-baseline.php',
+                ],
+                $basePath
+            );
+
+            $this->assertSame(0, $exitCode, $output);
+            $this->assertStringContainsString(
+                'Generated baseline [structarmed-baseline.php] with 1 violation(s).',
+                $output
+            );
+            $this->assertStringContainsString(
+                '    public function handle(): void',
+                (string) file_get_contents($basePath . '/src/Foo.php')
+            );
+
+            $baseline = file_get_contents($basePath . '/structarmed-baseline.php');
+
+            $this->assertIsString($baseline);
+            $this->assertStringContainsString("'rule' => 'source.class_name_must_have_suffix'", $baseline);
+            $this->assertStringContainsString("'message' => 'Class [App\\Foo] must have suffix [Service]'", $baseline);
+            $this->assertStringNotContainsString('source.must_declare_method_visibility', $baseline);
+        } finally {
+            $this->removeTempDirectory($basePath);
+        }
+    }
+
     public function testAnalyseCommandReportsBaselineGenerationFailure(): void
     {
         $basePath = $this->createProjectDirectoryWithViolation();
@@ -748,6 +920,50 @@ public function testAnalyseCommandReportsConfiguredBaselineFailure(): void
         }
     }
 
+    public function testAnalyseCommandReportsConfiguredBaselineFailureBeforeFix(): void
+    {
+        $basePath = $this->createProjectDirectoryWithImplicitMethodVisibilityViolation();
+
+        try {
+            file_put_contents($basePath . '/structarmed.php', <<<'PHP'
+<?php
+
+declare(strict_types=1);
+
+use Boundwize\StructArmed\Architecture;
+use Boundwize\StructArmed\Rule\Rules\Class_\MustDeclareMethodVisibilityRule;
+
+return Architecture::define()
+    ->baseline('missing-baseline.php')
+    ->layer('Source', 'src/')
+    ->rule('source.must_declare_method_visibility', new MustDeclareMethodVisibilityRule('Source'));
+PHP);
+
+            [$exitCode, $output] = $this->runApplication(
+                [
+                    'structarmed',
+                    'analyse',
+                    '--config=' . $basePath . '/structarmed.php',
+                    '--fix',
+                    '--no-progress',
+                ],
+                $basePath
+            );
+
+            $this->assertSame(1, $exitCode);
+            $this->assertStringContainsString(
+                'Error: Baseline file [missing-baseline.php] does not exist.',
+                $output
+            );
+            $this->assertStringContainsString(
+                '    function handle(): void',
+                (string) file_get_contents($basePath . '/src/Foo.php')
+            );
+        } finally {
+            $this->removeTempDirectory($basePath);
+        }
+    }
+
     public function testAnalyseCommandReportsConfiguredBaselineFailureAfterFix(): void
     {
         $basePath = $this->createProjectDirectoryWithViolation();