diff --git a/Sources/XcodeGenKit/PBXProjGenerator.swift b/Sources/XcodeGenKit/PBXProjGenerator.swift
index 4b7e3909..495f4fc7 100644
--- a/Sources/XcodeGenKit/PBXProjGenerator.swift
+++ b/Sources/XcodeGenKit/PBXProjGenerator.swift
@@ -67,7 +67,7 @@ public class PBXProjGenerator {
             let buildSettings = spec.getProjectBuildSettings(config: config)
             var baseConfigurationReference: String?
             if let configPath = spec.configFiles[config.name] {
-                baseConfigurationReference = sourceGenerator.getFileReference(path: spec.basePath + configPath, inPath: spec.basePath)
+                baseConfigurationReference = sourceGenerator.getContainedFileReference(path: spec.basePath + configPath)
             }
             return XCBuildConfiguration(reference: referenceGenerator.generate(XCBuildConfiguration.self, config.name), name: config.name, baseConfigurationReference: baseConfigurationReference, buildSettings: buildSettings)
         }
@@ -225,7 +225,7 @@ public class PBXProjGenerator {
 
             var baseConfigurationReference: String?
             if let configPath = target.configFiles[config.name] {
-                baseConfigurationReference = sourceGenerator.getFileReference(path: spec.basePath + configPath, inPath: spec.basePath)
+                baseConfigurationReference =  sourceGenerator.getContainedFileReference(path: spec.basePath + configPath)
             }
             return XCBuildConfiguration(reference: referenceGenerator.generate(XCBuildConfiguration.self, config.name + target.name), name: config.name, baseConfigurationReference: baseConfigurationReference, buildSettings: buildSettings)
         }
diff --git a/Sources/XcodeGenKit/SourceGenerator.swift b/Sources/XcodeGenKit/SourceGenerator.swift
index 27409708..c410915a 100644
--- a/Sources/XcodeGenKit/SourceGenerator.swift
+++ b/Sources/XcodeGenKit/SourceGenerator.swift
@@ -65,6 +65,19 @@ class SourceGenerator {
         return SourceFile(path: path, fileReference: fileReference, buildFile: buildFile, buildPhase: buildPhase)
     }
 
+    func getContainedFileReference(path: Path) -> String {
+        let createIntermediateGroups = spec.options.createIntermediateGroups
+
+        let parentPath = path.parent()
+        let fileReference = getFileReference(path: path, inPath: parentPath)
+        let parentGroup = getGroup(path: parentPath, mergingChildren: [fileReference], createIntermediateGroups: createIntermediateGroups, isBaseGroup: true)
+
+        if createIntermediateGroups {
+            createIntermediaGroups(for: parentGroup.reference, at: parentPath)
+        }
+        return fileReference
+    }
+
     func getFileReference(path: Path, inPath: Path, name: String? = nil, sourceTree: PBXSourceTree = .group) -> String {
         if let fileReference = fileReferencesByPath[path] {
             return fileReference