diff --git a/phpunit/src/CompilerBaseApiTest.php b/phpunit/src/CompilerBaseApiTest.php
index d8175ac6..32049290 100644
--- a/phpunit/src/CompilerBaseApiTest.php
+++ b/phpunit/src/CompilerBaseApiTest.php
@@ -1003,14 +1003,60 @@ sources:
   - main.php
 YAML);
 
-        $files = $this->invokeMethod('parseProjectYaml', $projectFile);
+        $files = $this->compiler->getFiles($projectFile);
         $entry = realpath(dirname($projectFile) . '/main.php');
 
         $this->assertSame([], $files);
         $this->assertSame($entry, $this->getPropertyValue('sapiEntryFile'));
         $this->assertSame([$entry], $this->getPropertyValue('embeddedFiles'));
         $this->assertSame([$entry], $this->getPropertyValue('embeddedPhpFiles'));
-        $this->invokeMethod('validateLoadedProjectConfiguration');
+    }
+
+    public function testEntryWithoutCliIsIgnoredAndRemainsAnAotSource(): void
+    {
+        $projectFile = $this->createProjectFile(<<<'YAML'
+sapi: embed
+entry: main.php
+sources:
+  - main.php
+YAML);
+        $entry = realpath(dirname($projectFile) . '/main.php');
+
+        $climate = $this->getPropertyValue('climate');
+        $climate->output->defaultTo('buffer');
+        $files = $this->compiler->getFiles($projectFile);
+        $output = $climate->output->get('buffer')->get();
+
+        $this->assertStringContainsString(
+            '`entry` is ignored because `sapi` does not contain cli',
+            $output,
+        );
+        $this->assertSame([$entry], $files);
+        $this->assertNull($this->getPropertyValue('sapiEntryFile'));
+        $this->assertSame([], $this->getPropertyValue('embeddedFiles'));
+        $this->assertSame([], $this->getPropertyValue('embeddedPhpFiles'));
+    }
+
+    public function testMissingEntryWithoutCliIsIgnoredBeforeFileValidation(): void
+    {
+        $projectFile = $this->createProjectFile(<<<'YAML'
+sapi: fpm
+php-builder: {}
+entry: missing.php
+sources:
+  - main.php
+YAML);
+        $climate = $this->getPropertyValue('climate');
+        $climate->output->defaultTo('buffer');
+
+        $files = $this->compiler->getFiles($projectFile);
+
+        $this->assertSame([realpath(dirname($projectFile) . '/main.php')], $files);
+        $this->assertStringContainsString(
+            '`entry` is ignored because `sapi` does not contain cli',
+            $climate->output->get('buffer')->get(),
+        );
+        $this->assertNull($this->getPropertyValue('sapiEntryFile'));
     }
 
     public function testCommandLineEntryConfiguresPhpBuilderCliSapi(): void
diff --git a/src/Build/SourcePipelineTrait.php b/src/Build/SourcePipelineTrait.php
index f3286fbd..51d95dab 100644
--- a/src/Build/SourcePipelineTrait.php
+++ b/src/Build/SourcePipelineTrait.php
@@ -521,11 +521,33 @@ trait SourcePipelineTrait
         if ($this->isSapiBuild() && !$this->isPhpBuilderBuild()) {
             $this->error('The cli and fpm SAPIs require `php-builder`');
         }
-        if ($this->hasSapi('cli') && $this->sapiEntryFile === null) {
+        if ($this->hasSapi('cli') && $this->sapiEntryConfiguredPath === null) {
             $this->error('`sapi` containing cli requires an `entry` PHP file');
         }
-        if ($this->sapiEntryFile !== null && !$this->hasSapi('cli')) {
-            $this->error('`entry` requires `sapi` to contain cli');
+        if ($this->sapiEntryConfiguredPath !== null && !$this->hasSapi('cli')) {
+            $this->climate->warning('`entry` is ignored because `sapi` does not contain cli');
+            $this->sapiEntryFile = null;
+            $this->sapiEntryConfiguredPath = null;
+            $this->sapiEntryConfiguredValue = null;
+        }
+        if ($this->sapiEntryConfiguredPath !== null) {
+            $entry = realpath($this->sapiEntryConfiguredPath);
+            if ($entry === false || !is_file($entry)) {
+                $value = $this->sapiEntryConfiguredValue ?? $this->sapiEntryConfiguredPath;
+                $this->error('Entry file does not exist: `' . $value . '`');
+            }
+            if (!FileScanner::isPhpFile($entry) || str_ends_with($entry, '.stub.php')) {
+                $this->error('`entry` must select an executable PHP file');
+            }
+            $this->sapiEntryFile = $entry;
+            if (!in_array($this->sapiEntryFile, $this->embeddedFiles, true)) {
+                $this->embeddedFiles[] = $this->sapiEntryFile;
+                sort($this->embeddedFiles, SORT_STRING);
+            }
+            if (!in_array($this->sapiEntryFile, $this->embeddedPhpFiles, true)) {
+                $this->embeddedPhpFiles[] = $this->sapiEntryFile;
+                sort($this->embeddedPhpFiles, SORT_STRING);
+            }
         }
         if ($this->embeddedFiles !== [] && !$this->isBuildModeBin() && !$this->isSapiBuild()) {
             $this->error('`embedded-files` requires `mode: bin`');
diff --git a/src/CompilerBase.php b/src/CompilerBase.php
index 9118e113..b70827d7 100644
--- a/src/CompilerBase.php
+++ b/src/CompilerBase.php
@@ -563,8 +563,12 @@ class CompilerBase implements PropertyAccessContext
     /** @var list<string> */
     protected array $phpBuilderExtensions = [];
 
-    /** Absolute path of the embedded primary script used by the CLI SAPI. */
+    /** Canonical path of the active embedded primary script used by the CLI SAPI. */
     protected ?string $sapiEntryFile = null;
+    /** Resolved entry candidate awaiting validation against the final SAPI selection. */
+    protected ?string $sapiEntryConfiguredPath = null;
+    /** Original entry spelling retained for diagnostics. */
+    protected ?string $sapiEntryConfiguredValue = null;
     protected ?string $sapiPhpSourceDirectory = null;
     protected ?string $sapiPhpBuildDirectory = null;
     protected ?string $sapiPhpPrefix = null;
diff --git a/src/Translator.php b/src/Translator.php
index e060d909..b07379bc 100644
--- a/src/Translator.php
+++ b/src/Translator.php
@@ -4392,9 +4392,6 @@ CODE;
                 }
             }
         }
-        if ($this->sapiEntryFile !== null) {
-            $this->embeddedFiles[] = $this->sapiEntryFile;
-        }
         $this->embeddedFiles = array_values(array_unique($this->embeddedFiles));
         sort($this->embeddedFiles, SORT_STRING);
         $this->embeddedPhpFiles = array_values(array_filter(
@@ -4685,11 +4682,7 @@ CODE;
             $this->resourceConfig['manifest'] = $manifest;
         }
 
-        $list = $this->filterIgnoredFiles($list);
-        if ($this->sapiEntryFile !== null) {
-            $list = array_values(array_diff($list, [$this->sapiEntryFile]));
-        }
-        return $list;
+        return $this->filterIgnoredFiles($list);
     }
 
     private function configurePhpBuilder(PhpBuilderConfiguration $configuration): void
@@ -4707,21 +4700,12 @@ CODE;
             $this->error('`entry` must be a non-empty PHP file path');
         }
         $value = trim($value);
-        $entryPath = $this->resolvePath($value, $baseDirectory, 'Entry path');
-        $entry = realpath($entryPath);
-        if ($entry === false || !is_file($entry)) {
-            $this->error('Entry file does not exist: `' . $value . '`');
-        }
-        if (!FileScanner::isPhpFile($entry) || str_ends_with($entry, '.stub.php')) {
-            $this->error('`entry` must select an executable PHP file');
-        }
-        $this->sapiEntryFile = $entry;
-        if (!in_array($entry, $this->embeddedFiles, true)) {
-            $this->embeddedFiles[] = $entry;
-        }
-        if (!in_array($entry, $this->embeddedPhpFiles, true)) {
-            $this->embeddedPhpFiles[] = $entry;
-        }
+        // Existence and file-type checks are deliberately deferred until the
+        // final SAPI selection is known. Command-line --sapi may override YAML,
+        // and entry has no semantics unless that final selection contains CLI.
+        $this->sapiEntryConfiguredValue = $value;
+        $this->sapiEntryConfiguredPath = $this->resolvePath($value, $baseDirectory, 'Entry path');
+        $this->sapiEntryFile = null;
     }
 
     private function configureSapiTargets(string|array $value): void