diff --git a/ssg/build_yaml.py b/ssg/build_yaml.py
index 5f0d3a41d772..7e55341838b0 100644
--- a/ssg/build_yaml.py
+++ b/ssg/build_yaml.py
@@ -893,6 +893,7 @@ class Rule(XCCDFEntity, Templatable):
         rationale=lambda: "",
         severity=lambda: "",
         references=lambda: dict(),
+        control_references=lambda: dict(),
         components=lambda: list(),
         identifiers=lambda: dict(),
         ocil_clause=lambda: None,
@@ -1212,16 +1213,23 @@ def _add_ident_elements(self, rule):
             ident.set("system", SSG_IDENT_URIS[ident_type])
             ident.text = ident_val
 
-    def add_extra_reference(self, ref_type, ref_value):
-        if ref_type in self.references:
-            if ref_value in self.references[ref_type]:
+    def add_control_reference(self, ref_type, ref_value):
+        if ref_type in self.control_references:
+            if ref_value in self.control_references[ref_type]:
                 msg = (
                     "Rule %s already contains a '%s' reference with value '%s'." % (
                         self.id_, ref_type, ref_value))
                 raise ValueError(msg)
-            self.references[ref_type].append(ref_value)
+            self.control_references[ref_type].append(ref_value)
         else:
-            self.references[ref_type] = [ref_value]
+            self.control_references[ref_type] = [ref_value]
+
+    def merge_control_references(self):
+        for ref_type in self.control_references:
+            if ref_type in self.references:
+                self.references[ref_type].append(self.control_references[ref_type])
+            else:
+                self.references[ref_type] = self.control_references[ref_type]
 
     def to_xml_element(self, env_yaml=None):
         rule = ET.Element('{%s}Rule' % XCCDF12_NS)
diff --git a/ssg/controls.py b/ssg/controls.py
index 68268dbb7ed6..1450ec5bdeb4 100644
--- a/ssg/controls.py
+++ b/ssg/controls.py
@@ -184,7 +184,7 @@ def add_references(self, reference_type, rules):
             if not rule:
                 continue
             try:
-                rule.add_extra_reference(reference_type, self.id)
+                rule.add_control_reference(reference_type, self.id)
             except ValueError as exc:
                 msg = (
                     "Please remove any duplicate listing of rule '%s' in "
@@ -527,5 +527,13 @@ def save_everything(self, output_dir):
             policy.dump_yaml(filename)
 
     def add_references(self, rules):
+        # First we add all control references into a separate attribute
         for policy in self.policies.values():
             policy.add_references(rules)
+        # Then we unify them under references attribute
+        # This allows multiple control files to add references of the same type, and still track what references already existed in the rule.
+        self._merge_references(rules)
+
+    def _merge_references(self, rules):
+        for rule in rules.values():
+            rule.merge_control_references()