diff --git a/src/harness/unittests/tsserverProjectSystem.ts b/src/harness/unittests/tsserverProjectSystem.ts
index e1ac647c2ac..dbf9bf670e6 100644
--- a/src/harness/unittests/tsserverProjectSystem.ts
+++ b/src/harness/unittests/tsserverProjectSystem.ts
@@ -3068,9 +3068,11 @@ namespace ts.projectSystem {
             projectService.openClientFile(file1.path);
 
             const project = projectService.inferredProjects[0];
-            const sourceFile = project.getSourceFile(<Path>file1.path);
-            assert.isTrue("test" in sourceFile.resolvedModules);
-            assert.equal((<ResolvedModule>sourceFile.resolvedModules["test"]).resolvedFileName, moduleFile.path);
+            const sourceFileForFile1 = project.getSourceFile(<Path>file1.path);
+            const sourceFileForModuleFile = project.getSourceFile(<Path>moduleFile.path);
+
+            assert.isNotNull(sourceFileForFile1);
+            assert.isNotNull(sourceFileForModuleFile);
         });
     });
 
diff --git a/src/server/editorServices.ts b/src/server/editorServices.ts
index 23b172d1cfe..eba0dbb119c 100644
--- a/src/server/editorServices.ts
+++ b/src/server/editorServices.ts
@@ -1072,6 +1072,10 @@ namespace ts.server {
                 ? this.inferredProjects[0]
                 : new InferredProject(this, this.documentRegistry, this.compilerOptionsForInferredProjects);
 
+            if (root.scriptKind === ScriptKind.JS || root.scriptKind === ScriptKind.JSX) {
+                project.isJsInferredProject = true;
+            }
+
             project.addRoot(root);
 
             this.directoryWatchers.startWatchingContainingDirectoriesForFile(
@@ -1079,12 +1083,6 @@ namespace ts.server {
                 project,
                 fileName => this.onConfigFileAddedForInferredProject(fileName));
 
-            if (root.scriptKind === ScriptKind.JS || root.scriptKind === ScriptKind.JSX) {
-                const options = project.getCompilerOptions();
-                options.maxNodeModuleJsDepth = 2;
-                project.setCompilerOptions(options);
-            }
-
             project.updateGraph();
 
             if (!useExistingProject) {
diff --git a/src/server/project.ts b/src/server/project.ts
index 6085ee05159..ca3950a48a8 100644
--- a/src/server/project.ts
+++ b/src/server/project.ts
@@ -566,9 +566,6 @@ namespace ts.server {
 
         setCompilerOptions(compilerOptions: CompilerOptions) {
             if (compilerOptions) {
-                if (this.projectKind === ProjectKind.Inferred) {
-                    compilerOptions.allowJs = true;
-                }
                 compilerOptions.allowNonTsExtensions = true;
                 if (changesAffectModuleResolution(this.compilerOptions, compilerOptions)) {
                     // reset cached unresolved imports if changes in compiler options affected module resolution
@@ -715,6 +712,26 @@ namespace ts.server {
             }
         })();
 
+        private _isJsInferredProject = false;
+        set isJsInferredProject(newValue: boolean) {
+            if (newValue && !this._isJsInferredProject) {
+                this.setCompilerOptions(this.getCompilerOptions());
+            }
+            this._isJsInferredProject = newValue;
+        }
+
+        setCompilerOptions(newOptions: CompilerOptions) {
+            if (!newOptions) {
+                return;
+            }
+
+            if (this._isJsInferredProject && typeof newOptions.maxNodeModuleJsDepth !== "number") {
+                newOptions.maxNodeModuleJsDepth = 2;
+            }
+            newOptions.allowJs = true;
+            super.setCompilerOptions(newOptions);
+        }
+
         // Used to keep track of what directories are watched for this project
         directoriesWatchedForTsconfig: string[] = [];