diff --git a/.changeset/tall-beans-shave.md b/.changeset/tall-beans-shave.md
new file mode 100644
index 0000000000..74725a9dd7
--- /dev/null
+++ b/.changeset/tall-beans-shave.md
@@ -0,0 +1,6 @@
+---
+"@medusajs/product": patch
+"@medusajs/utils": patch
+---
+
+fix(product, utils): handle metadata key deletion on product update
diff --git a/integration-tests/http/__tests__/product/admin/product.spec.ts b/integration-tests/http/__tests__/product/admin/product.spec.ts
index 172b2c8d95..b9144823dc 100644
--- a/integration-tests/http/__tests__/product/admin/product.spec.ts
+++ b/integration-tests/http/__tests__/product/admin/product.spec.ts
@@ -1912,7 +1912,7 @@ medusaIntegrationTestRunner({
 
           const payload = {
             metadata: {
-              "test-key": "",
+              "test-key": "", // item is deleted by setting to empty string
               "test-key-2": null,
             },
           }
@@ -1924,13 +1924,11 @@ medusaIntegrationTestRunner({
           )
 
           expect(response.status).toEqual(200)
-          expect(response.data.product.metadata).toEqual(
-            // BREAKING: Metadata updates are all-or-nothing in v2
-            {
-              "test-key": "",
-              "test-key-2": null,
-            }
-          )
+          expect(response.data.product.metadata).toEqual({
+            // "test-key" is deleted
+            "test-key-2": null, // updated
+            "test-key-3": "test-value-3", // preserved
+          })
         })
 
         it("updates products sales channels", async () => {
diff --git a/packages/core/utils/src/common/index.ts b/packages/core/utils/src/common/index.ts
index b024d57fd8..b3fb55eba4 100644
--- a/packages/core/utils/src/common/index.ts
+++ b/packages/core/utils/src/common/index.ts
@@ -72,7 +72,6 @@ export * from "./resolve-exports"
 export * from "./rules"
 export * from "./selector-constraints-to-string"
 export * from "./serialize-error"
-export * from "./set-metadata"
 export * from "./simple-hash"
 export * from "./string-to-select-relation-object"
 export * from "./stringify-circular"
diff --git a/packages/core/utils/src/common/set-metadata.ts b/packages/core/utils/src/common/set-metadata.ts
deleted file mode 100644
index 4dc5f6d42a..0000000000
--- a/packages/core/utils/src/common/set-metadata.ts
+++ /dev/null
@@ -1,45 +0,0 @@
-import { MedusaError } from "./errors"
-
-/**
- * Dedicated method to set metadata.
- * @param obj - the entity to apply metadata to.
- * @param metadata - the metadata to set
- * @return resolves to the updated result.
- */
-export function setMetadata(
-  obj: { metadata: Record<string, unknown> | null },
-  metadata: Record<string, unknown>
-): Record<string, unknown> {
-  const existing = obj.metadata || {}
-  const newData = {}
-
-  for (const [key, value] of Object.entries(metadata)) {
-    if (typeof key !== "string") {
-      throw new MedusaError(
-        MedusaError.Types.INVALID_ARGUMENT,
-        "Key type is invalid. Metadata keys must be strings"
-      )
-    }
-
-    /**
-     * We reserve the empty string as a way to delete a key.
-     * If the value is an empty string, we don't
-     * set it, and if it exists in the existing metadata, we
-     * unset the field.
-     */
-    if (value === "") {
-      if (key in existing) {
-        delete existing[key]
-      }
-
-      continue
-    }
-
-    newData[key] = value
-  }
-
-  return {
-    ...existing,
-    ...newData,
-  }
-}
diff --git a/packages/modules/product/src/repositories/product.ts b/packages/modules/product/src/repositories/product.ts
index 1c4990c8f4..fc1e4ee220 100644
--- a/packages/modules/product/src/repositories/product.ts
+++ b/packages/modules/product/src/repositories/product.ts
@@ -6,6 +6,8 @@ import {
   buildQuery,
   DALUtils,
   MedusaError,
+  isPresent,
+  mergeMetadata,
 } from "@medusajs/framework/utils"
 import { SqlEntityManager, wrap } from "@mikro-orm/postgresql"
 
@@ -148,6 +150,10 @@ export class ProductRepository extends DALUtils.mikroOrmBaseRepositoryFactory(
         )
       }
 
+      if (isPresent(productToUpdate.metadata)) {
+        productToUpdate.metadata = mergeMetadata(product.metadata ?? {}, productToUpdate.metadata)
+      }
+
       wrappedProduct.assign(productToUpdate)
     }