diff --git a/engine/common/src/main/java/org/enso/common/ContextFactory.java b/engine/common/src/main/java/org/enso/common/ContextFactory.java
index 796ab95c3ba3..afafec92a3f0 100644
--- a/engine/common/src/main/java/org/enso/common/ContextFactory.java
+++ b/engine/common/src/main/java/org/enso/common/ContextFactory.java
@@ -30,6 +30,7 @@
  * @param options additional options for the Context
  * @param executionEnvironment optional name of the execution environment to use during execution
  * @param warningsLimit maximal number of warnings reported to the user
+ * @param checkForWarnings name of method to check for warnings
  */
 public final class ContextFactory {
   private String projectRoot;
@@ -47,6 +48,7 @@ public final class ContextFactory {
   private boolean useGlobalIrCacheLocation = true;
   private boolean enableAutoParallelism;
   private String executionEnvironment;
+  private String checkForWarnings;
   private int warningsLimit = 100;
   private java.util.Map<String, String> options = java.util.Collections.emptyMap();
 
@@ -141,6 +143,11 @@ public ContextFactory options(Map<String, String> options) {
     return this;
   }
 
+    public ContextFactory checkForWarnings(String fqnOfMethod) {
+      this.checkForWarnings = fqnOfMethod;
+      return this;
+    }
+
   public Context build() {
     if (executionEnvironment != null) {
       options.put("enso.ExecutionEnvironment", executionEnvironment);
@@ -169,6 +176,9 @@ public Context build() {
             .out(out)
             .err(err)
             .in(in);
+    if (checkForWarnings != null) {
+      builder.option("enso-debug-server.fn", checkForWarnings);
+    }
     if (messageTransport != null) {
       builder.serverTransport(messageTransport);
     }
diff --git a/engine/runner/src/main/java/org/enso/runner/Main.java b/engine/runner/src/main/java/org/enso/runner/Main.java
index 212b612f3e18..b6f79f88b0bf 100644
--- a/engine/runner/src/main/java/org/enso/runner/Main.java
+++ b/engine/runner/src/main/java/org/enso/runner/Main.java
@@ -688,6 +688,25 @@ private void handleRun(
     }
     var projectMode = fileAndProject._1();
     var file = fileAndProject._2();
+    var mainFile = file;
+    if (projectMode) {
+      var result = PackageManager$.MODULE$.Default().loadPackage(file);
+      if (result.isSuccess()) {
+        var s = (scala.util.Success) result;
+        @SuppressWarnings("unchecked")
+        var pkg = (org.enso.pkg.Package<java.io.File>) s.get();
+
+        mainFile = pkg.mainFile();
+        if (!mainFile.exists()) {
+          println("Main file does not exist.");
+          throw exitFail();
+        }
+      } else {
+        println(((scala.util.Failure) result).exception().getMessage());
+        throw exitFail();
+      }
+    }
+
     var projectRoot = fileAndProject._3();
     var options = new HashMap<String, String>();
 
@@ -699,6 +718,7 @@ private void handleRun(
             .enableIrCaches(enableIrCaches)
             .disablePrivateCheck(disablePrivateCheck)
             .strictErrors(true)
+            .checkForWarnings(mainFile.getName().replace(".enso", "") + ".main")
             .enableAutoParallelism(enableAutoParallelism)
             .enableStaticAnalysis(enableStaticAnalysis)
             .executionEnvironment(executionEnvironment != null ? executionEnvironment : "live")
@@ -724,12 +744,6 @@ private void handleRun(
         var s = (scala.util.Success) result;
         @SuppressWarnings("unchecked")
         var pkg = (org.enso.pkg.Package<java.io.File>) s.get();
-        var main = pkg.mainFile();
-        if (!main.exists()) {
-          println("Main file does not exist.");
-          context.context().close();
-          throw exitFail();
-        }
         var mainModuleName = pkg.moduleNameForFile(pkg.mainFile()).toString();
         runPackage(context, mainModuleName, file, additionalArgs);
       } else {