diff --git a/prdoc/pr_6382.prdoc b/prdoc/pr_6382.prdoc
new file mode 100644
index 000000000000..ac6821c1100a
--- /dev/null
+++ b/prdoc/pr_6382.prdoc
@@ -0,0 +1,12 @@
+title: 'gensis-config: patching default `RuntimeGenesisConfig` fixed'
+doc:
+- audience: Node Dev
+  description: |-
+    This PR fixes issue reported in #6306.
+    It changes the behavior of `sc_chain_spec::json_patch::merge` function which no longer removes any keys from the base JSON object.
+
+crates:
+- name: staging-chain-spec-builder
+  bump: major
+- name: sc-chain-spec
+  bump: major
diff --git a/substrate/bin/utils/chain-spec-builder/src/lib.rs b/substrate/bin/utils/chain-spec-builder/src/lib.rs
index 6f3128ed7eb0..73c2868b3312 100644
--- a/substrate/bin/utils/chain-spec-builder/src/lib.rs
+++ b/substrate/bin/utils/chain-spec-builder/src/lib.rs
@@ -261,19 +261,19 @@ impl ChainSpecBuilder {
 						.map_err(|e| format!("Conversion to json failed: {e}"))?;
 
 				// We want to extract only raw genesis ("genesis::raw" key), and apply it as a patch
-				// for the original json file. However, the file also contains original plain
-				// genesis ("genesis::runtimeGenesis") so set it to null so the patch will erase it.
+				// for the original json file.
 				genesis_json.as_object_mut().map(|map| {
 					map.retain(|key, _| key == "genesis");
-					map.get_mut("genesis").map(|genesis| {
-						genesis.as_object_mut().map(|genesis_map| {
-							genesis_map
-								.insert("runtimeGenesis".to_string(), serde_json::Value::Null);
-						});
-					});
 				});
 
 				let mut org_chain_spec_json = extract_chain_spec_json(input_chain_spec.as_path())?;
+
+				// The original plain genesis ("genesis::runtimeGenesis") is no longer needed, so
+				// just remove it:
+				org_chain_spec_json
+					.get_mut("genesis")
+					.and_then(|genesis| genesis.as_object_mut())
+					.and_then(|genesis| genesis.remove("runtimeGenesis"));
 				json_patch::merge(&mut org_chain_spec_json, genesis_json);
 
 				let chain_spec_json = serde_json::to_string_pretty(&org_chain_spec_json)
diff --git a/substrate/client/chain-spec/src/genesis_config_builder.rs b/substrate/client/chain-spec/src/genesis_config_builder.rs
index 66989495d423..5fe8f9dc053c 100644
--- a/substrate/client/chain-spec/src/genesis_config_builder.rs
+++ b/substrate/client/chain-spec/src/genesis_config_builder.rs
@@ -142,11 +142,9 @@ where
 	/// The patching process modifies the default `RuntimeGenesisConfig` according to the following
 	/// rules:
 	/// 1. Existing keys in the default configuration will be overridden by the corresponding values
-	///    in the patch.
+	///    in the patch (also applies to `null` values).
 	/// 2. If a key exists in the patch but not in the default configuration, it will be added to
 	///    the resulting `RuntimeGenesisConfig`.
-	/// 3. Keys in the default configuration that have null values in the patch will be removed from
-	///    the resulting `RuntimeGenesisConfig`. This is helpful for changing enum variant value.
 	///
 	/// Please note that the patch may contain full `RuntimeGenesisConfig`.
 	pub fn get_storage_for_patch(&self, patch: Value) -> core::result::Result<Storage, String> {
diff --git a/substrate/client/chain-spec/src/json_patch.rs b/substrate/client/chain-spec/src/json_patch.rs
index c3930069a60d..a223792374e0 100644
--- a/substrate/client/chain-spec/src/json_patch.rs
+++ b/substrate/client/chain-spec/src/json_patch.rs
@@ -22,9 +22,10 @@ use serde_json::Value;
 
 /// Recursively merges two JSON objects, `a` and `b`, into a single object.
 ///
-/// If a key exists in both objects, the value from `b` will override the value from `a`.
-/// If a key exists in `b` with a `null` value, it will be removed from `a`.
+/// If a key exists in both objects, the value from `b` will override the value from `a` (also if
+/// value in `b` is `null`).
 /// If a key exists only in `b` and not in `a`, it will be added to `a`.
+/// No keys will be removed from `a`.
 ///
 /// # Arguments
 ///
@@ -34,11 +35,7 @@ pub fn merge(a: &mut Value, b: Value) {
 	match (a, b) {
 		(Value::Object(a), Value::Object(b)) =>
 			for (k, v) in b {
-				if v.is_null() {
-					a.remove(&k);
-				} else {
-					merge(a.entry(k).or_insert(Value::Null), v);
-				}
+				merge(a.entry(k).or_insert(Value::Null), v);
 			},
 		(a, b) => *a = b,
 	};
@@ -166,7 +163,7 @@ mod tests {
 	}
 
 	#[test]
-	fn test6_patch_removes_keys_if_null() {
+	fn test6_patch_does_not_remove_keys_if_null() {
 		let mut j1 = json!({
 			"a": {
 				"name": "xxx",
@@ -186,6 +183,16 @@ mod tests {
 		});
 
 		merge(&mut j1, j2);
-		assert_eq!(j1, json!({ "a": {"name":"xxx", "value":456, "enum_variant_2": 32 }}));
+		assert_eq!(
+			j1,
+			json!({
+				"a": {
+					"name":"xxx",
+					"value":456,
+					"enum_variant_1": null,
+					"enum_variant_2": 32
+				}
+			})
+		);
 	}
 }