diff --git a/smithy-typescript-codegen/src/main/java/software/amazon/smithy/typescript/codegen/PackageJsonGenerator.java b/smithy-typescript-codegen/src/main/java/software/amazon/smithy/typescript/codegen/PackageJsonGenerator.java
index 9190b8a0184..bb35c9d4298 100644
--- a/smithy-typescript-codegen/src/main/java/software/amazon/smithy/typescript/codegen/PackageJsonGenerator.java
+++ b/smithy-typescript-codegen/src/main/java/software/amazon/smithy/typescript/codegen/PackageJsonGenerator.java
@@ -21,6 +21,7 @@
 import software.amazon.smithy.codegen.core.SymbolDependency;
 import software.amazon.smithy.model.node.Node;
 import software.amazon.smithy.model.node.ObjectNode;
+import software.amazon.smithy.typescript.codegen.util.MergeJsonNodes;
 import software.amazon.smithy.utils.IoUtils;
 import software.amazon.smithy.utils.SmithyInternalApi;
 
@@ -43,9 +44,11 @@ static void writePackageJson(
     ) {
         // Write the package.json file.
         InputStream resource = PackageJsonGenerator.class.getResourceAsStream("base-package.json");
-        ObjectNode node = Node.parse(IoUtils.toUtf8String(resource))
-                        .expectObjectNode()
-                        .merge(settings.getPackageJson());
+        ObjectNode node = MergeJsonNodes.mergeWithScripts(
+            Node.parse(IoUtils.toUtf8String(resource))
+                .expectObjectNode(),
+            settings.getPackageJson()
+        );
 
         // Merge TypeScript dependencies into the package.json file.
         for (Map.Entry<String, Map<String, SymbolDependency>> depEntry : dependencies.entrySet()) {
diff --git a/smithy-typescript-codegen/src/main/java/software/amazon/smithy/typescript/codegen/util/MergeJsonNodes.java b/smithy-typescript-codegen/src/main/java/software/amazon/smithy/typescript/codegen/util/MergeJsonNodes.java
new file mode 100644
index 00000000000..80a7ff4a40c
--- /dev/null
+++ b/smithy-typescript-codegen/src/main/java/software/amazon/smithy/typescript/codegen/util/MergeJsonNodes.java
@@ -0,0 +1,42 @@
+/*
+ * Copyright Amazon.com, Inc. or its affiliates. All Rights Reserved.
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+package software.amazon.smithy.typescript.codegen.util;
+
+import java.util.Objects;
+import software.amazon.smithy.model.node.ObjectNode;
+
+
+public final class MergeJsonNodes {
+
+    private MergeJsonNodes() {}
+
+    /**
+     * @param left - original node.
+     * @param right - overwriting node.
+     * @return new node with shallow merged fields except the recursively merged "scripts" field.
+     */
+    public static ObjectNode mergeWithScripts(ObjectNode left, ObjectNode right) {
+        Objects.requireNonNull(left);
+        Objects.requireNonNull(right);
+
+        ObjectNode.Builder merged = left.toBuilder();
+        right.getMembers().forEach((k, v) -> {
+            String key = k.getValue();
+            if (left.containsMember(key)) {
+                if (left.getMember(key).get().isObjectNode() && v.isObjectNode() && key.equals("scripts")) {
+                    merged.withMember(key,
+                        MergeJsonNodes.mergeWithScripts(left.expectObjectMember(key), v.expectObjectNode())
+                    );
+                } else {
+                    merged.withMember(key, v);
+                }
+            } else {
+                merged.withMember(key, v);
+            }
+        });
+        return merged.build();
+    }
+}
diff --git a/smithy-typescript-codegen/src/test/java/software/amazon/smithy/typescript/codegen/util/MergeJsonNodesTest.java b/smithy-typescript-codegen/src/test/java/software/amazon/smithy/typescript/codegen/util/MergeJsonNodesTest.java
new file mode 100644
index 00000000000..9be1f46a3f5
--- /dev/null
+++ b/smithy-typescript-codegen/src/test/java/software/amazon/smithy/typescript/codegen/util/MergeJsonNodesTest.java
@@ -0,0 +1,104 @@
+package software.amazon.smithy.typescript.codegen.util;
+
+import org.junit.jupiter.api.Test;
+import software.amazon.smithy.model.node.Node;
+import software.amazon.smithy.model.node.ObjectNode;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+class MergeJsonNodesTest {
+
+    @Test
+    void apply() {
+        ObjectNode left = ObjectNode.parse("""
+            {
+                "name": "hello, world",
+                "version": 5,
+                "scripts": {
+                    "target": "exec",
+                    "target2": "exec2",
+                    "args": ["a", "b", "c"],
+                    "nested": {
+                        "deep": "."
+                    }
+                },
+                "metadata": {
+                    "A": "A",
+                    "B": "B",
+                    "C": "C"
+                }
+            }
+            """).expectObjectNode();
+
+        ObjectNode right = ObjectNode.parse("""
+            {
+                "version": 6,
+                "scripts": {
+                    "target": "no-op",
+                    "args": ["a", "b", "c", "d"],
+                    "nested": {
+                        "option": "b"
+                    }
+                },
+                "metadata": {
+                    "A": "A"
+                }
+            }
+            """).expectObjectNode();
+
+        ObjectNode expected = ObjectNode.parse("""
+            {
+                "name": "hello, world",
+                "version": 6,
+                "scripts": {
+                    "target": "no-op",
+                    "target2": "exec2",
+                    "args": ["a", "b", "c", "d"],
+                    "nested": {
+                        "deep": ".",
+                        "option": "b"
+                    }
+                },
+                "metadata": {
+                    "A": "A"
+                }
+            }
+            """).expectObjectNode();
+
+        ObjectNode l = expected;
+        ObjectNode r = MergeJsonNodes.mergeWithScripts(left, right);
+
+        assertEquals(
+            l.expectStringMember("name"),
+            r.expectStringMember("name")
+        );
+        assertEquals(
+            l.expectNumberMember("version"),
+            r.expectNumberMember("version")
+        );
+        assertEquals(
+            l.expectObjectMember("scripts").expectStringMember("target"),
+            r.expectObjectMember("scripts").expectStringMember("target")
+        );
+        assertEquals(
+            l.expectObjectMember("scripts").expectStringMember("target2"),
+            r.expectObjectMember("scripts").expectStringMember("target2")
+        );
+        assertEquals(
+            l.expectObjectMember("scripts").expectArrayMember("args").getElementsAs(Node::toString),
+            r.expectObjectMember("scripts").expectArrayMember("args").getElementsAs(Node::toString)
+        );
+        assertEquals(
+            l.expectObjectMember("scripts").expectObjectMember("nested").expectStringMember("option"),
+            r.expectObjectMember("scripts").expectObjectMember("nested").expectStringMember("option")
+        );
+        assertEquals(
+            1,
+            r.expectObjectMember("scripts").expectObjectMember("nested").getStringMap().size()
+        );
+        assertEquals(
+            1,
+            r.expectObjectMember("metadata").getStringMap().size()
+        );
+    }
+}
\ No newline at end of file