diff --git a/src/plugins/qmakeprojectmanager/makefileparse.cpp b/src/plugins/qmakeprojectmanager/makefileparse.cpp
index 206270f481f..17e140f82e4 100644
--- a/src/plugins/qmakeprojectmanager/makefileparse.cpp
+++ b/src/plugins/qmakeprojectmanager/makefileparse.cpp
@@ -126,13 +126,12 @@ void dumpQMakeAssignments(const QList<QMakeAssignment> &list)
     }
 }
 
-void MakeFileParse::parseAssignments(QList<QMakeAssignment> *assignments)
+QList<QMakeAssignment> MakeFileParse::parseAssignments(const QList<QMakeAssignment> &assignments)
 {
     bool foundSeparateDebugInfo = false;
     bool foundForceDebugInfo = false;
-    QList<QMakeAssignment> oldAssignments = *assignments;
-    assignments->clear();
-    foreach (const QMakeAssignment &qa, oldAssignments) {
+    QList<QMakeAssignment> filteredAssignments;
+    foreach (const QMakeAssignment &qa, assignments) {
         if (qa.variable == QLatin1String("CONFIG")) {
             QStringList values = qa.value.split(QLatin1Char(' '));
             QStringList newValues;
@@ -218,10 +217,10 @@ void MakeFileParse::parseAssignments(QList<QMakeAssignment> *assignments)
             if (!newValues.isEmpty()) {
                 QMakeAssignment newQA = qa;
                 newQA.value = newValues.join(QLatin1Char(' '));
-                assignments->append(newQA);
+                filteredAssignments.append(newQA);
             }
         } else {
-            assignments->append(qa);
+            filteredAssignments.append(qa);
         }
     }
 
@@ -233,15 +232,16 @@ void MakeFileParse::parseAssignments(QList<QMakeAssignment> *assignments)
         newQA.variable = QLatin1String("CONFIG");
         newQA.op = QLatin1String("+=");
         newQA.value = QLatin1String("force_debug_info");
-        assignments->append(newQA);
+        filteredAssignments.append(newQA);
     } else if (foundSeparateDebugInfo) {
         // Found only separate_debug_info, so readd it
         QMakeAssignment newQA;
         newQA.variable = QLatin1String("CONFIG");
         newQA.op = QLatin1String("+=");
         newQA.value = QLatin1String("separate_debug_info");
-        assignments->append(newQA);
+        filteredAssignments.append(newQA);
     }
+    return filteredAssignments;
 }
 
 static FilePath findQMakeBinaryFromMakefile(const QString &makefile)
@@ -270,7 +270,7 @@ static FilePath findQMakeBinaryFromMakefile(const QString &makefile)
     return FilePath();
 }
 
-MakeFileParse::MakeFileParse(const QString &makefile)
+MakeFileParse::MakeFileParse(const QString &makefile, Mode mode) : m_mode(mode)
 {
     qCDebug(logging()) << "Parsing makefile" << makefile;
     if (!QFileInfo::exists(makefile)) {
@@ -367,9 +367,9 @@ void MakeFileParse::parseCommandLine(const QString &command, const QString &proj
     dumpQMakeAssignments(assignments);
 
     // Filter out CONFIG arguments we know into m_qmakeBuildConfig and m_config
-    parseAssignments(&assignments);
+    const QList<QMakeAssignment> filteredAssignments = parseAssignments(assignments);
     qCDebug(logging()) << "  After parsing";
-    dumpQMakeAssignments(assignments);
+    dumpQMakeAssignments(filteredAssignments);
 
     qCDebug(logging()) << "  Explicit Debug" << m_qmakeBuildConfig.explicitDebug;
     qCDebug(logging()) << "  Explicit Release" << m_qmakeBuildConfig.explicitRelease;
@@ -385,7 +385,9 @@ void MakeFileParse::parseCommandLine(const QString &command, const QString &proj
                        << (m_config.separateDebugInfo == TriState::Enabled);
 
     // Create command line of all unfiltered arguments
-    foreach (const QMakeAssignment &qa, assignments)
+    const QList<QMakeAssignment> &assignmentsToUse = m_mode == Mode::FilterKnownConfigValues
+            ? filteredAssignments : assignments;
+    foreach (const QMakeAssignment &qa, assignmentsToUse)
         QtcProcess::addArg(&m_unparsedArguments, qa.variable + qa.op + qa.value);
     if (!afterAssignments.isEmpty()) {
         QtcProcess::addArg(&m_unparsedArguments, QLatin1String("-after"));
@@ -517,7 +519,7 @@ void QmakeProjectManagerPlugin::testMakefileParser()
     QFETCH(bool, separateDebugInfo);
     QFETCH(int, effectiveBuildConfig);
 
-    MakeFileParse parser("/tmp/something");
+    MakeFileParse parser("/tmp/something", MakeFileParse::Mode::FilterKnownConfigValues);
     parser.parseCommandLine(command, project);
 
     QCOMPARE(Utils::QtcProcess::splitArgs(parser.unparsedArguments()),
diff --git a/src/plugins/qmakeprojectmanager/makefileparse.h b/src/plugins/qmakeprojectmanager/makefileparse.h
index 90d34156620..87613188edd 100644
--- a/src/plugins/qmakeprojectmanager/makefileparse.h
+++ b/src/plugins/qmakeprojectmanager/makefileparse.h
@@ -42,7 +42,8 @@ struct QMakeAssignment
 class MakeFileParse
 {
 public:
-    MakeFileParse(const QString &makefile);
+    enum class Mode { FilterKnownConfigValues, DoNotFilterKnownConfigValues };
+    MakeFileParse(const QString &makefile, Mode mode);
 
     enum MakefileState { MakefileMissing, CouldNotParse, Okay };
 
@@ -63,7 +64,7 @@ public:
 private:
     void parseArgs(const QString &args, const QString &project,
                    QList<QMakeAssignment> *assignments, QList<QMakeAssignment> *afterAssignments);
-    void parseAssignments(QList<QMakeAssignment> *assignments);
+    QList<QMakeAssignment> parseAssignments(const QList<QMakeAssignment> &assignments);
 
     class QmakeBuildConfig
     {
@@ -74,6 +75,7 @@ private:
         bool explicitNoBuildAll = false;
     };
 
+    const Mode m_mode;
     MakefileState m_state;
     Utils::FilePath m_qmakePath;
     QString m_srcProFile;
diff --git a/src/plugins/qmakeprojectmanager/qmakebuildconfiguration.cpp b/src/plugins/qmakeprojectmanager/qmakebuildconfiguration.cpp
index b15557e8654..3d3ec6af01d 100644
--- a/src/plugins/qmakeprojectmanager/qmakebuildconfiguration.cpp
+++ b/src/plugins/qmakeprojectmanager/qmakebuildconfiguration.cpp
@@ -490,7 +490,7 @@ QmakeBuildConfiguration::MakefileState QmakeBuildConfiguration::compareToImportF
     qCDebug(logs) << "QMakeBuildConfiguration::compareToImport";
 
     QMakeStep *qs = qmakeStep();
-    MakeFileParse parse(makefile);
+    MakeFileParse parse(makefile, MakeFileParse::Mode::DoNotFilterKnownConfigValues);
 
     if (parse.makeFileState() == MakeFileParse::MakefileMissing) {
         qCDebug(logs) << "**Makefile missing";
@@ -546,10 +546,12 @@ QmakeBuildConfiguration::MakefileState QmakeBuildConfiguration::compareToImportF
     // and compare that on its own
     QString workingDirectory = QFileInfo(makefile).absolutePath();
     QStringList actualArgs;
-    QString userArgs = macroExpander()->expandProcessArgs(qs->userArguments());
-    // This copies the settings from userArgs to actualArgs (minus some we
+    QString allArgs = macroExpander()->expandProcessArgs(qs->allArguments(
+        QtKitAspect::qtVersion(target()->kit()), QMakeStep::ArgumentFlag::Expand));
+    // This copies the settings from allArgs to actualArgs (minus some we
     // are not interested in), splitting them up into individual strings:
-    extractSpecFromArguments(&userArgs, workingDirectory, version, &actualArgs);
+    extractSpecFromArguments(&allArgs, workingDirectory, version, &actualArgs);
+    actualArgs.removeFirst(); // Project file.
     const QString actualSpec = qs->mkspec();
 
     QString qmakeArgs = parse.unparsedArguments();
diff --git a/src/plugins/qmakeprojectmanager/qmakeprojectimporter.cpp b/src/plugins/qmakeprojectmanager/qmakeprojectimporter.cpp
index ba4b9d8601c..3fec5661f11 100644
--- a/src/plugins/qmakeprojectmanager/qmakeprojectimporter.cpp
+++ b/src/plugins/qmakeprojectmanager/qmakeprojectimporter.cpp
@@ -126,7 +126,7 @@ QList<void *> QmakeProjectImporter::examineDirectory(const FilePath &importPath)
         qCDebug(logs) << "  Parsing makefile" << file;
         // find interesting makefiles
         QString makefile = importPath.toString() + QLatin1Char('/') + file;
-        MakeFileParse parse(makefile);
+        MakeFileParse parse(makefile, MakeFileParse::Mode::FilterKnownConfigValues);
         if (parse.makeFileState() != MakeFileParse::Okay) {
             qCDebug(logs) << "  Parsing the makefile failed" << makefile;
             continue;