diff --git a/src/Composer/Command/ConfigCommand.php b/src/Composer/Command/ConfigCommand.php
index cbdc174bc..b625cbf1a 100644
--- a/src/Composer/Command/ConfigCommand.php
+++ b/src/Composer/Command/ConfigCommand.php
@@ -771,8 +771,12 @@ EOT
                     foreach ($bits as $bit) {
                         $currentValue = $currentValue[$bit] ?? null;
                     }
-                    if (is_array($currentValue)) {
-                        $value = array_merge($currentValue, $value);
+                    if (is_array($currentValue) && is_array($value)) {
+                        if (array_is_list($currentValue) && array_is_list($value)) {
+                            $value = array_merge($currentValue, $value);
+                        } else {
+                            $value = $value + $currentValue;
+                        }
                     }
                 }
             }
diff --git a/src/Composer/Json/JsonManipulator.php b/src/Composer/Json/JsonManipulator.php
index 8d6759671..809cea57a 100644
--- a/src/Composer/Json/JsonManipulator.php
+++ b/src/Composer/Json/JsonManipulator.php
@@ -416,6 +416,9 @@ class JsonManipulator
             if ($subName !== null) {
                 $curVal = json_decode($children, true);
                 unset($curVal[$name][$subName]);
+                if ($curVal[$name] === []) {
+                    $curVal[$name] = new \ArrayObject();
+                }
                 $this->addSubNode($mainNode, $name, $curVal[$name]);
             }
 
@@ -427,7 +430,7 @@ class JsonManipulator
             if ($subName !== null) {
                 $curVal = json_decode($matches['content'], true);
                 unset($curVal[$name][$subName]);
-                $childrenClean = $this->format($curVal);
+                $childrenClean = $this->format($curVal, 0, true);
             }
 
             return $matches['start'] . $childrenClean . $matches['end'];
@@ -534,12 +537,19 @@ class JsonManipulator
     /**
      * @param mixed $data
      */
-    public function format($data, int $depth = 0): string
+    public function format($data, int $depth = 0, bool $wasObject = false): string
     {
-        if (is_array($data)) {
-            reset($data);
+        if ($data instanceof \stdClass || $data instanceof \ArrayObject) {
+            $data = (array) $data;
+            $wasObject = true;
+        }
 
-            if (is_numeric(key($data))) {
+        if (is_array($data)) {
+            if (\count($data) === 0) {
+                return $wasObject ? '{' . $this->newline . str_repeat($this->indent, $depth + 1) . '}' : '[]';
+            }
+
+            if (array_is_list($data)) {
                 foreach ($data as $key => $val) {
                     $data[$key] = $this->format($val, $depth + 1);
                 }
@@ -550,7 +560,7 @@ class JsonManipulator
             $out = '{' . $this->newline;
             $elems = [];
             foreach ($data as $key => $val) {
-                $elems[] = str_repeat($this->indent, $depth + 2) . JsonFile::encode($key). ': '.$this->format($val, $depth + 1);
+                $elems[] = str_repeat($this->indent, $depth + 2) . JsonFile::encode((string) $key). ': '.$this->format($val, $depth + 1);
             }
 
             return $out . implode(','.$this->newline, $elems) . $this->newline . str_repeat($this->indent, $depth + 1) . '}';
diff --git a/tests/Composer/Test/Command/ConfigCommandTest.php b/tests/Composer/Test/Command/ConfigCommandTest.php
index 68653c622..27ee92b4a 100644
--- a/tests/Composer/Test/Command/ConfigCommandTest.php
+++ b/tests/Composer/Test/Command/ConfigCommandTest.php
@@ -82,6 +82,26 @@ class ConfigCommandTest extends TestCase
             ['setting-key' => 'preferred-install.foo/*', '--unset' => true],
             ['config' => ['preferred-install' => []]],
         ];
+        yield 'set extra with merge' => [
+            [],
+            ['setting-key' => 'extra.patches.foo/bar', 'setting-value' => ['{"123":"value"}'], '--json' => true, '--merge' => true],
+            ['extra' => ['patches' => ['foo/bar' => [123 => 'value']]]],
+        ];
+        yield 'combine extra with merge' => [
+            ['extra' => ['patches' => ['foo/bar' => [5 => 'oldvalue']]]],
+            ['setting-key' => 'extra.patches.foo/bar', 'setting-value' => ['{"123":"value"}'], '--json' => true, '--merge' => true],
+            ['extra' => ['patches' => ['foo/bar' => [123 => 'value', 5 => 'oldvalue']]]],
+        ];
+        yield 'combine extra with list' => [
+            ['extra' => ['patches' => ['foo/bar' => ['oldvalue']]]],
+            ['setting-key' => 'extra.patches.foo/bar', 'setting-value' => ['{"123":"value"}'], '--json' => true, '--merge' => true],
+            ['extra' => ['patches' => ['foo/bar' => [123 => 'value', 0 => 'oldvalue']]]],
+        ];
+        yield 'overwrite extra with merge' => [
+            ['extra' => ['patches' => ['foo/bar' => [123 => 'oldvalue']]]],
+            ['setting-key' => 'extra.patches.foo/bar', 'setting-value' => ['{"123":"value"}'], '--json' => true, '--merge' => true],
+            ['extra' => ['patches' => ['foo/bar' => [123 => 'value']]]],
+        ];
     }
 
     /**
diff --git a/tests/Composer/Test/Json/JsonManipulatorTest.php b/tests/Composer/Test/Json/JsonManipulatorTest.php
index 8ee8b5862..1d27069bd 100644
--- a/tests/Composer/Test/Json/JsonManipulatorTest.php
+++ b/tests/Composer/Test/Json/JsonManipulatorTest.php
@@ -1721,6 +1721,38 @@ class JsonManipulatorTest extends TestCase
 ', $manipulator->getContents());
     }
 
+    public function testRemoveSubNodePreservesObjectTypeWhenEmpty(): void
+    {
+        $manipulator = new JsonManipulator('{
+    "test": {"0": "foo"}
+}');
+
+        $this->assertTrue($manipulator->removeSubNode('test', '0'));
+        $this->assertEquals('{
+    "test": {
+    }
+}
+', $manipulator->getContents());
+    }
+
+    public function testRemoveSubNodePreservesObjectTypeWhenEmpty2(): void
+    {
+        $manipulator = new JsonManipulator('{
+    "config": {
+        "preferred-install": {"foo/*": "source"}
+    }
+}');
+
+        $this->assertTrue($manipulator->removeConfigSetting('preferred-install.foo/*'));
+        $this->assertEquals('{
+    "config": {
+        "preferred-install": {
+        }
+    }
+}
+', $manipulator->getContents());
+    }
+
     public function testAddSubNodeInRequire(): void
     {
         $manipulator = new JsonManipulator('{