diff --git a/keyboards/argyle/keyboard.json b/keyboards/argyle/keyboard.json
index a7bfc335df9..d97f067be8b 100755
--- a/keyboards/argyle/keyboard.json
+++ b/keyboards/argyle/keyboard.json
@@ -11,7 +11,6 @@
     },
     "matrix_pins": {
         "cols": ["D1", "D4", "D5", "D6", "D7", "B0", "NO_PIN", "NO_PIN", "NO_PIN", "NO_PIN", "NO_PIN", "NO_PIN", "NO_PIN", "NO_PIN"],
-        "custom": true,
         "custom_lite": true,
         "rows": ["D0", "C3", "B1", "B2", "B3"]
     },
diff --git a/keyboards/keychron/c2_pro/info.json b/keyboards/keychron/c2_pro/info.json
index 9c0e1ac72eb..8a7d0968b14 100644
--- a/keyboards/keychron/c2_pro/info.json
+++ b/keyboards/keychron/c2_pro/info.json
@@ -26,7 +26,6 @@
     "matrix_pins": {
         "cols": ["A10", "A9", "A8", "B1", "B0", "A7", "A6", "A5", "A4", "A3", "A2", "NO_PIN", "NO_PIN", "NO_PIN", "NO_PIN", "NO_PIN", "NO_PIN", "NO_PIN", "NO_PIN", "C14"],
         "rows": ["B5", "B4", "B3", "A15", "A14", "A13"],
-        "custom": true,
         "custom_lite": true
     },
     "diode_direction": "ROW2COL"
diff --git a/keyboards/keychron/q1v2/info.json b/keyboards/keychron/q1v2/info.json
index f0342254fac..ba6f908bbbe 100644
--- a/keyboards/keychron/q1v2/info.json
+++ b/keyboards/keychron/q1v2/info.json
@@ -27,7 +27,6 @@
     "matrix_pins": {
         "cols": ["C14", "C15", "A0", "A1", "A2", "A3", "A4", "A5", null, null, null, null, null, null, null, null],
         "rows": ["B5", "B4", "B3", "A15", "A14", "A13"],
-        "custom": true,
         "custom_lite": true
     },
     "diode_direction": "ROW2COL",
diff --git a/lib/python/qmk/cli/generate/rules_mk.py b/lib/python/qmk/cli/generate/rules_mk.py
index 358a22fd1d7..16084bded18 100755
--- a/lib/python/qmk/cli/generate/rules_mk.py
+++ b/lib/python/qmk/cli/generate/rules_mk.py
@@ -96,11 +96,10 @@ def generate_rules_mk(cli):
         rules_mk_lines.append(generate_rule('SPLIT_TRANSPORT', 'custom'))
 
     # Set CUSTOM_MATRIX, if needed
-    if kb_info_json.get('matrix_pins', {}).get('custom'):
-        if kb_info_json.get('matrix_pins', {}).get('custom_lite'):
-            rules_mk_lines.append(generate_rule('CUSTOM_MATRIX', 'lite'))
-        else:
-            rules_mk_lines.append(generate_rule('CUSTOM_MATRIX', 'yes'))
+    if kb_info_json.get('matrix_pins', {}).get('custom_lite'):
+        rules_mk_lines.append(generate_rule('CUSTOM_MATRIX', 'lite'))
+    elif kb_info_json.get('matrix_pins', {}).get('custom'):
+        rules_mk_lines.append(generate_rule('CUSTOM_MATRIX', 'yes'))
 
     if converter:
         rules_mk_lines.append(generate_rule('CONVERT_TO', converter))
diff --git a/lib/python/qmk/info.py b/lib/python/qmk/info.py
index b4fa481b1bc..dccbb69ea44 100644
--- a/lib/python/qmk/info.py
+++ b/lib/python/qmk/info.py
@@ -302,6 +302,24 @@ def _extract_features(info_data, rules):
     return info_data
 
 
+def _extract_matrix_rules(info_data, rules):
+    """Find all the features enabled in rules.mk.
+    """
+    if rules.get('CUSTOM_MATRIX', 'no') != 'no':
+        if 'matrix_pins' in info_data and 'custom' in info_data['matrix_pins']:
+            _log_warning(info_data, 'Custom Matrix is specified in both info.json and rules.mk, the rules.mk values win.')
+
+        if 'matrix_pins' not in info_data:
+            info_data['matrix_pins'] = {}
+
+        if rules['CUSTOM_MATRIX'] == 'lite':
+            info_data['matrix_pins']['custom_lite'] = True
+        else:
+            info_data['matrix_pins']['custom'] = True
+
+    return info_data
+
+
 def _pin_name(pin):
     """Returns the proper representation for a pin.
     """
@@ -549,7 +567,6 @@ def _extract_matrix_info(info_data, config_c):
     row_pins = config_c.get('MATRIX_ROW_PINS', '').replace('{', '').replace('}', '').strip()
     col_pins = config_c.get('MATRIX_COL_PINS', '').replace('{', '').replace('}', '').strip()
     direct_pins = config_c.get('DIRECT_PINS', '').replace(' ', '')[1:-1]
-    info_snippet = {}
 
     if 'MATRIX_ROWS' in config_c and 'MATRIX_COLS' in config_c:
         if 'matrix_size' in info_data:
@@ -564,26 +581,20 @@ def _extract_matrix_info(info_data, config_c):
         if 'matrix_pins' in info_data and 'cols' in info_data['matrix_pins'] and 'rows' in info_data['matrix_pins']:
             _log_warning(info_data, 'Matrix pins are specified in both info.json and config.h, the config.h values win.')
 
-        info_snippet['cols'] = _extract_pins(col_pins)
-        info_snippet['rows'] = _extract_pins(row_pins)
+        if 'matrix_pins' not in info_data:
+            info_data['matrix_pins'] = {}
+
+        info_data['matrix_pins']['cols'] = _extract_pins(col_pins)
+        info_data['matrix_pins']['rows'] = _extract_pins(row_pins)
 
     if direct_pins:
         if 'matrix_pins' in info_data and 'direct' in info_data['matrix_pins']:
             _log_warning(info_data, 'Direct pins are specified in both info.json and config.h, the config.h values win.')
 
-        info_snippet['direct'] = _extract_direct_matrix(direct_pins)
+        if 'matrix_pins' not in info_data:
+            info_data['matrix_pins'] = {}
 
-    if config_c.get('CUSTOM_MATRIX', 'no') != 'no':
-        if 'matrix_pins' in info_data and 'custom' in info_data['matrix_pins']:
-            _log_warning(info_data, 'Custom Matrix is specified in both info.json and config.h, the config.h values win.')
-
-        info_snippet['custom'] = True
-
-        if config_c['CUSTOM_MATRIX'] == 'lite':
-            info_snippet['custom_lite'] = True
-
-    if info_snippet:
-        info_data['matrix_pins'] = info_snippet
+        info_data['matrix_pins']['direct'] = _extract_direct_matrix(direct_pins)
 
     return info_data
 
@@ -752,6 +763,7 @@ def _extract_rules_mk(info_data, rules):
 
     # Merge in config values that can't be easily mapped
     _extract_features(info_data, rules)
+    _extract_matrix_rules(info_data, rules)
 
     return info_data