diff --git a/dist/setup/index.js b/dist/setup/index.js
index b53c01a8..1a27fe9d 100644
--- a/dist/setup/index.js
+++ b/dist/setup/index.js
@@ -82997,28 +82997,43 @@ async function useCpythonVersion(version, architecture, updateEnvironment, check
             installDir = tc.find('Python', semanticVersionSpec, architecture);
         }
     }
-    if (!installDir) {
-        // Try system Python as fallback (e.g., on architectures without pre-built binaries)
-        try {
-            const { exitCode, stdout } = await exec.getExecOutput('python3', [
-                '-c',
-                'import sys; print(sys.prefix)'
-            ]);
-            if (exitCode === 0) {
-                const systemPrefix = stdout.trim();
-                const systemVersion = await exec.getExecOutput('python3', [
+    if (!installDir && !freethreaded) {
+        // Try system Python as fallback, but only for architectures that have
+        // no pre-built binaries in the manifest at all. This prevents the
+        // fallback from firing when a specific version is missing on a
+        // supported architecture (e.g., requesting Python 3.99 on x86_64).
+        const baseArchitecture = architecture.replace('-freethreaded', '');
+        if (!manifest) {
+            manifest = await installer.getManifest();
+        }
+        const archHasManifestEntries = manifest?.some(release => release.files?.some((file) => file.arch === baseArchitecture));
+        if (!archHasManifestEntries) {
+            try {
+                const sysInfo = await exec.getExecOutput('python3', [
                     '-c',
-                    'import sys; print(f"{sys.version_info.major}.{sys.version_info.minor}.{sys.version_info.micro}")'
+                    'import sys, os; print(sys.executable + "\\n" + f"{sys.version_info.major}.{sys.version_info.minor}.{sys.version_info.micro}" + "\\n" + sys.prefix + "\\n" + os.path.dirname(sys.executable))'
                 ]);
-                if (systemVersion.exitCode === 0 &&
-                    semver.satisfies(systemVersion.stdout.trim(), semanticVersionSpec)) {
-                    installDir = systemPrefix;
-                    core.warning(`Pre-built Python not available for architecture '${architecture}'. Using system Python ${systemVersion.stdout.trim()} at ${systemPrefix}.`);
+                if (sysInfo.exitCode === 0) {
+                    const [sysExecutable, sysVersion, sysPrefix, sysBinDir] = sysInfo.stdout.trim().split('\n');
+                    if (semver.satisfies(sysVersion, semanticVersionSpec)) {
+                        core.warning(`Pre-built Python not available for architecture '${baseArchitecture}'. Using system Python ${sysVersion} at ${sysExecutable}.`);
+                        if (updateEnvironment) {
+                            core.exportVariable('pythonLocation', sysPrefix);
+                            core.exportVariable('PKG_CONFIG_PATH', sysPrefix + '/lib/pkgconfig');
+                            core.exportVariable('Python_ROOT_DIR', sysPrefix);
+                            core.exportVariable('Python2_ROOT_DIR', sysPrefix);
+                            core.exportVariable('Python3_ROOT_DIR', sysPrefix);
+                            core.addPath(sysBinDir);
+                        }
+                        core.setOutput('python-version', sysVersion);
+                        core.setOutput('python-path', sysExecutable);
+                        return { impl: 'CPython', version: sysVersion };
+                    }
                 }
             }
-        }
-        catch {
-            // System Python not available, fall through to error
+            catch {
+                // System Python not available, fall through to error
+            }
         }
     }
     if (!installDir) {
diff --git a/src/find-python.ts b/src/find-python.ts
index 9e8de0da..ed1187ce 100644
--- a/src/find-python.ts
+++ b/src/find-python.ts
@@ -122,31 +122,57 @@ export async function useCpythonVersion(
     }
   }
 
-  if (!installDir) {
-    // Try system Python as fallback (e.g., on architectures without pre-built binaries)
-    try {
-      const {exitCode, stdout} = await exec.getExecOutput('python3', [
-        '-c',
-        'import sys; print(sys.prefix)'
-      ]);
-      if (exitCode === 0) {
-        const systemPrefix = stdout.trim();
-        const systemVersion = await exec.getExecOutput('python3', [
+  if (!installDir && !freethreaded) {
+    // Try system Python as fallback, but only for architectures that have
+    // no pre-built binaries in the manifest at all. This prevents the
+    // fallback from firing when a specific version is missing on a
+    // supported architecture (e.g., requesting Python 3.99 on x86_64).
+    const baseArchitecture = architecture.replace('-freethreaded', '');
+    if (!manifest) {
+      manifest = await installer.getManifest();
+    }
+    const archHasManifestEntries = manifest?.some(
+      release =>
+        release.files?.some(
+          (file: {arch: string}) => file.arch === baseArchitecture
+        )
+    );
+
+    if (!archHasManifestEntries) {
+      try {
+        const sysInfo = await exec.getExecOutput('python3', [
           '-c',
-          'import sys; print(f"{sys.version_info.major}.{sys.version_info.minor}.{sys.version_info.micro}")'
+          'import sys, os; print(sys.executable + "\\n" + f"{sys.version_info.major}.{sys.version_info.minor}.{sys.version_info.micro}" + "\\n" + sys.prefix + "\\n" + os.path.dirname(sys.executable))'
         ]);
-        if (
-          systemVersion.exitCode === 0 &&
-          semver.satisfies(systemVersion.stdout.trim(), semanticVersionSpec)
-        ) {
-          installDir = systemPrefix;
-          core.warning(
-            `Pre-built Python not available for architecture '${architecture}'. Using system Python ${systemVersion.stdout.trim()} at ${systemPrefix}.`
-          );
+        if (sysInfo.exitCode === 0) {
+          const [sysExecutable, sysVersion, sysPrefix, sysBinDir] =
+            sysInfo.stdout.trim().split('\n');
+          if (semver.satisfies(sysVersion, semanticVersionSpec)) {
+            core.warning(
+              `Pre-built Python not available for architecture '${baseArchitecture}'. Using system Python ${sysVersion} at ${sysExecutable}.`
+            );
+
+            if (updateEnvironment) {
+              core.exportVariable('pythonLocation', sysPrefix);
+              core.exportVariable(
+                'PKG_CONFIG_PATH',
+                sysPrefix + '/lib/pkgconfig'
+              );
+              core.exportVariable('Python_ROOT_DIR', sysPrefix);
+              core.exportVariable('Python2_ROOT_DIR', sysPrefix);
+              core.exportVariable('Python3_ROOT_DIR', sysPrefix);
+              core.addPath(sysBinDir);
+            }
+
+            core.setOutput('python-version', sysVersion);
+            core.setOutput('python-path', sysExecutable);
+
+            return {impl: 'CPython', version: sysVersion};
+          }
         }
+      } catch {
+        // System Python not available, fall through to error
       }
-    } catch {
-      // System Python not available, fall through to error
     }
   }