diff --git a/bin/phunkie b/bin/phunkie
index b1e0b9a..21a5784 100755
--- a/bin/phunkie
+++ b/bin/phunkie
@@ -85,6 +85,7 @@ use function Phunkie\Console\Functions\{setColors, printBanner, loadHistory, sav
 
     if (isset($args[1]) && !str_starts_with($args[1], '-')) {
         $className = $args[1];
+
         if (class_exists($className) && is_subclass_of($className, IOApp::class)) {
             $app = new $className();
         }
diff --git a/tests/Acceptance/ReplSteps.php b/tests/Acceptance/ReplSteps.php
index 7a3db2d..15cf9a0 100644
--- a/tests/Acceptance/ReplSteps.php
+++ b/tests/Acceptance/ReplSteps.php
@@ -44,24 +44,33 @@ public function __construct()
 
     private function startRepl(string $command = 'php bin/phunkie'): void
     {
-        if ($command !== 'php bin/phunkie' && $command !== 'php bin/phunkie -c') {
+        $isIOAppCommand = $command !== 'php bin/phunkie' && $command !== 'php bin/phunkie -c';
+
+        if ($isIOAppCommand) {
             // Non-standard command means we need to test the actual process
             $this->useProcessManager = true;
         }
 
         if ($this->useProcessManager) {
             $this->processManager->start($command);
-            $stdout = $this->processManager->getStdout();
-            if ($stdout !== null) {
-                $newOutput = ReplOutputReader::readOutput($stdout);
-                $this->output .= $newOutput;
-            }
-            // Also capture stderr for debugging
-            $stderr = $this->processManager->getStderr();
-            if ($stderr !== null) {
-                $errorOutput = ReplOutputReader::readOutput($stderr);
-                if ($errorOutput !== '') {
-                    $this->output .= "\n[STDERR]: " . $errorOutput;
+
+            if ($isIOAppCommand) {
+                // For IOApp commands, wait for the process to complete and capture all output
+                $this->waitForProcessAndCaptureOutput();
+            } else {
+                // For REPL mode, read available output
+                $stdout = $this->processManager->getStdout();
+                if ($stdout !== null) {
+                    $newOutput = ReplOutputReader::readOutput($stdout);
+                    $this->output .= $newOutput;
+                }
+                // Also capture stderr for debugging
+                $stderr = $this->processManager->getStderr();
+                if ($stderr !== null) {
+                    $errorOutput = ReplOutputReader::readOutput($stderr);
+                    if ($errorOutput !== '') {
+                        $this->output .= "\n[STDERR]: " . $errorOutput;
+                    }
                 }
             }
         } else {
@@ -71,6 +80,66 @@ private function startRepl(string $command = 'php bin/phunkie'): void
         }
     }
 
+    private function waitForProcessAndCaptureOutput(): void
+    {
+        $stdout = $this->processManager->getStdout();
+        $stderr = $this->processManager->getStderr();
+
+        // Wait for the process to complete (up to 5 seconds)
+        $maxWait = 5.0;
+        $startTime = microtime(true);
+
+        while ((microtime(true) - $startTime) < $maxWait) {
+            // Read any available stdout
+            if ($stdout !== null) {
+                $read = [$stdout];
+                $write = null;
+                $except = null;
+                if (stream_select($read, $write, $except, 0, 100000) > 0) { // 100ms timeout
+                    $chunk = stream_get_contents($stdout);
+                    if ($chunk !== false && $chunk !== '') {
+                        $this->output .= $chunk;
+                    }
+                }
+            }
+
+            // Read any available stderr
+            if ($stderr !== null) {
+                $read = [$stderr];
+                $write = null;
+                $except = null;
+                if (stream_select($read, $write, $except, 0, 10000) > 0) { // 10ms timeout
+                    $chunk = stream_get_contents($stderr);
+                    if ($chunk !== false && $chunk !== '') {
+                        $this->output .= "\n[STDERR]: " . $chunk;
+                    }
+                }
+            }
+
+            // Check if process has exited
+            $status = $this->processManager->getStatus();
+            if ($status !== null && !$status['running']) {
+                // Process has exited, read any remaining output
+                usleep(50000); // 50ms grace period for buffered output
+                if ($stdout !== null) {
+                    $remaining = stream_get_contents($stdout);
+                    if ($remaining !== false && $remaining !== '') {
+                        $this->output .= $remaining;
+                    }
+                }
+                if ($stderr !== null) {
+                    $remaining = stream_get_contents($stderr);
+                    if ($remaining !== false && $remaining !== '') {
+                        $this->output .= "\n[STDERR]: " . $remaining;
+                    }
+                }
+                break;
+            }
+
+            usleep(10000); // 10ms sleep between checks
+        }
+    }
+
     private function sendInput(string $input): void
     {
         // Check if input defines a class/function/trait/interface/enum
diff --git a/tests/Acceptance/Support/ReplProcessManager.php b/tests/Acceptance/Support/ReplProcessManager.php
index 640faca..024d5c7 100644
--- a/tests/Acceptance/Support/ReplProcessManager.php
+++ b/tests/Acceptance/Support/ReplProcessManager.php
@@ -80,6 +80,14 @@ public function isRunning(): bool
         return $this->process !== null;
     }
 
+    public function getStatus(): ?array
+    {
+        if ($this->process === null) {
+            return null;
+        }
+        return proc_get_status($this->process);
+    }
+
     public function terminate(): void
     {
         if ($this->process !== null) {