diff --git a/src/build-system.jam b/src/build-system.jam
index 8bbfe86d3..b79827bef 100644
--- a/src/build-system.jam
+++ b/src/build-system.jam
@@ -513,10 +513,10 @@ local rule should-clean-project ( project : detected-projects * )
         {
             r = true ;
         }
-        else
+        else if ! [ project.is-jamroot-module $(project) ]
         {
             local parent = [ project.attribute $(project) parent-module ] ;
-            if $(parent) && $(parent) != user-config
+            if $(parent)
             {
                 r = [ should-clean-project $(parent) : $(detected-projects) ] ;
             }
diff --git a/src/build/project.jam b/src/build/project.jam
index d947caf07..c345d8209 100644
--- a/src/build/project.jam
+++ b/src/build/project.jam
@@ -746,6 +746,16 @@ class project-attributes
         return $(self.$(attribute)) ;
     }
 
+    # Returns whether these attributes belong to a Jamroot project module.
+    #
+    rule is-jamroot ( )
+    {
+        if $(self.location) && $(self.project-root) = $(self.location)
+        {
+            return true ;
+        }
+    }
+
     # Prints the project attributes.
     #
     rule print ( )
@@ -811,6 +821,14 @@ rule attribute ( project attribute )
 }
 
 
+# Returns whether a project module is a Jamroot project module.
+#
+rule is-jamroot-module ( project )
+{
+    return [ $($(project).attributes).is-jamroot ] ;
+}
+
+
 # Returns the project target corresponding to the 'project-module'.
 #
 rule target ( project-module )