diff --git a/src/plugins/qmakeprojectmanager/qmakenodes.cpp b/src/plugins/qmakeprojectmanager/qmakenodes.cpp
index 5012d8e76e5..71f6ad1c4e5 100644
--- a/src/plugins/qmakeprojectmanager/qmakenodes.cpp
+++ b/src/plugins/qmakeprojectmanager/qmakenodes.cpp
@@ -1200,13 +1200,13 @@ void QmakePriFileNode::changeFiles(const QString &mimeType,
     if (!includeFile)
         return;
 
-    QDir priFileDir = QDir(m_qmakeProFileNode->m_projectDir);
 
     if (change == AddToProFile) {
         // Use the first variable for adding.
-        ProWriter::addFiles(includeFile, &lines, priFileDir, filePaths, varNameForAdding(mimeType));
+        ProWriter::addFiles(includeFile, &lines, filePaths, varNameForAdding(mimeType));
         notChanged->clear();
     } else { // RemoveFromProFile
+        QDir priFileDir = QDir(m_qmakeProFileNode->m_projectDir);
         *notChanged = ProWriter::removeFiles(includeFile, &lines, priFileDir, filePaths, varNamesForRemoving());
     }
 
diff --git a/src/shared/proparser/prowriter.cpp b/src/shared/proparser/prowriter.cpp
index 40eb243121e..1860a6a95f5 100644
--- a/src/shared/proparser/prowriter.cpp
+++ b/src/shared/proparser/prowriter.cpp
@@ -343,12 +343,15 @@ void ProWriter::putVarValues(ProFile *profile, QStringList *lines,
     }
 }
 
-void ProWriter::addFiles(ProFile *profile, QStringList *lines,
-    const QDir &proFileDir, const QStringList &values, const QString &var)
+void ProWriter::addFiles(ProFile *profile, QStringList *lines, const QStringList &values, const QString &var)
 {
     QStringList valuesToWrite;
+    QString prefixPwd;
+    QDir baseDir = QFileInfo(profile->fileName()).absoluteDir();
+    if (profile->fileName().endsWith(QLatin1String(".pri")))
+        prefixPwd = QLatin1String("$$PWD/");
     foreach (const QString &v, values)
-        valuesToWrite << proFileDir.relativeFilePath(v);
+        valuesToWrite << (prefixPwd + baseDir.relativeFilePath(v));
 
     putVarValues(profile, lines, valuesToWrite, var, AppendValues | MultiLine | AppendOperator);
 }
@@ -508,8 +511,25 @@ QStringList ProWriter::removeFiles(ProFile *profile, QStringList *lines,
     foreach (const QString &absoluteFilePath, values)
         valuesToFind << proFileDir.relativeFilePath(absoluteFilePath);
 
+    QStringList notYetChanged;
+    foreach (int i, removeVarValues(profile, lines, valuesToFind, vars))
+        notYetChanged.append(values.at(i));
+
+    if (!profile->fileName().endsWith(QLatin1String(".pri")))
+        return notYetChanged;
+
+    // If we didn't find them with a relative path to the .pro file
+    // maybe those files can be found via $$PWD/relativeToPriFile
+
+    valuesToFind.clear();
+    QDir baseDir = QFileInfo(profile->fileName()).absoluteDir();
+    QString prefixPwd = QLatin1String("$$PWD/");
+    foreach (const QString &absoluteFilePath, notYetChanged)
+        valuesToFind << (prefixPwd + baseDir.relativeFilePath(absoluteFilePath));
+
     QStringList notChanged;
     foreach (int i, removeVarValues(profile, lines, valuesToFind, vars))
-        notChanged.append(values.at(i));
+        notChanged.append(notYetChanged.at(i));
+
     return notChanged;
 }
diff --git a/src/shared/proparser/prowriter.h b/src/shared/proparser/prowriter.h
index bcb429f8882..d4ecad5b5ec 100644
--- a/src/shared/proparser/prowriter.h
+++ b/src/shared/proparser/prowriter.h
@@ -60,8 +60,7 @@ public:
     static QList<int> removeVarValues(ProFile *profile, QStringList *lines,
         const QStringList &values, const QStringList &vars);
 
-    static void addFiles(ProFile *profile, QStringList *lines,
-         const QDir &proFileDir, const QStringList &filePaths, const QString &var);
+    static void addFiles(ProFile *profile, QStringList *lines, const QStringList &filePaths, const QString &var);
     static QStringList removeFiles(ProFile *profile, QStringList *lines,
         const QDir &proFileDir, const QStringList &filePaths, const QStringList &vars);