diff --git a/.changeset/cyan-countries-brush.md b/.changeset/cyan-countries-brush.md
new file mode 100644
index 0000000000..cba8519534
--- /dev/null
+++ b/.changeset/cyan-countries-brush.md
@@ -0,0 +1,7 @@
+---
+"@medusajs/authentication": patch
+"@medusajs/pricing": patch
+"@medusajs/utils": patch
+---
+
+chore(utils): Update base repository to infer primary keys and support composite
diff --git a/packages/authentication/src/repositories/auth-provider.ts b/packages/authentication/src/repositories/auth-provider.ts
index a0d1d0f543..6445266d14 100644
--- a/packages/authentication/src/repositories/auth-provider.ts
+++ b/packages/authentication/src/repositories/auth-provider.ts
@@ -10,7 +10,12 @@ export class AuthProviderRepository extends DALUtils.mikroOrmBaseRepositoryFacto
   {
     create: RepositoryTypes.CreateAuthProviderDTO
   }
->(AuthProvider, "provider") {
+>(AuthProvider) {
+  constructor(...args: any[]) {
+    // @ts-ignore
+    super(...arguments)
+  }
+
   async update(
     data: RepositoryTypes.UpdateAuthProviderDTO[],
     context: Context = {}
diff --git a/packages/authentication/src/repositories/auth-user.ts b/packages/authentication/src/repositories/auth-user.ts
index 2da807aa41..6e5fa10f9c 100644
--- a/packages/authentication/src/repositories/auth-user.ts
+++ b/packages/authentication/src/repositories/auth-user.ts
@@ -8,6 +8,11 @@ import { SqlEntityManager } from "@mikro-orm/postgresql"
 export class AuthUserRepository extends DALUtils.mikroOrmBaseRepositoryFactory(
   AuthUser
 ) {
+  constructor(...args: any[]) {
+    // @ts-ignore
+    super(...arguments)
+  }
+
   async create(
     data: RepositoryTypes.CreateAuthUserDTO[],
     context: Context = {}
diff --git a/packages/cart/src/repositories/address.ts b/packages/cart/src/repositories/address.ts
index 994ff44221..53c375821e 100644
--- a/packages/cart/src/repositories/address.ts
+++ b/packages/cart/src/repositories/address.ts
@@ -10,6 +10,11 @@ export class AddressRepository extends DALUtils.mikroOrmBaseRepositoryFactory<
     create: CreateAddressDTO
   }
 >(Address) {
+  constructor(...args: any[]) {
+    // @ts-ignore
+    super(...arguments)
+  }
+
   async update(
     data: { address: Address; update: UpdateAddressDTO }[],
     context: Context = {}
diff --git a/packages/cart/src/repositories/cart.ts b/packages/cart/src/repositories/cart.ts
index 4aeddee7f3..952fc9fd1b 100644
--- a/packages/cart/src/repositories/cart.ts
+++ b/packages/cart/src/repositories/cart.ts
@@ -10,6 +10,11 @@ export class CartRepository extends DALUtils.mikroOrmBaseRepositoryFactory<
     create: CreateCartDTO
   }
 >(Cart) {
+  constructor(...args: any[]) {
+    // @ts-ignore
+    super(...arguments)
+  }
+
   async update(
     data: { cart: Cart; update: UpdateCartDTO }[],
     context: Context = {}
diff --git a/packages/pricing/src/repositories/currency.ts b/packages/pricing/src/repositories/currency.ts
index 1aa87a5319..7a15ded16b 100644
--- a/packages/pricing/src/repositories/currency.ts
+++ b/packages/pricing/src/repositories/currency.ts
@@ -9,4 +9,9 @@ export class CurrencyRepository extends DALUtils.mikroOrmBaseRepositoryFactory<
     create: RepositoryTypes.CreateCurrencyDTO
     update: RepositoryTypes.UpdateCurrencyDTO
   }
->(Currency, "code") {}
+>(Currency) {
+  constructor(...args: any[]) {
+    // @ts-ignore
+    super(...arguments)
+  }
+}
diff --git a/packages/pricing/src/repositories/money-amount.ts b/packages/pricing/src/repositories/money-amount.ts
index 66595fc592..c23c7fa070 100644
--- a/packages/pricing/src/repositories/money-amount.ts
+++ b/packages/pricing/src/repositories/money-amount.ts
@@ -9,4 +9,9 @@ export class MoneyAmountRepository extends DALUtils.mikroOrmBaseRepositoryFactor
     create: RepositoryTypes.CreateMoneyAmountDTO
     update: RepositoryTypes.UpdateMoneyAmountDTO
   }
->(MoneyAmount) {}
+>(MoneyAmount) {
+  constructor(...args: any[]) {
+    // @ts-ignore
+    super(...arguments)
+  }
+}
diff --git a/packages/pricing/src/repositories/price-list-rule-value.ts b/packages/pricing/src/repositories/price-list-rule-value.ts
index 6829876056..d1512834c0 100644
--- a/packages/pricing/src/repositories/price-list-rule-value.ts
+++ b/packages/pricing/src/repositories/price-list-rule-value.ts
@@ -10,6 +10,11 @@ export class PriceListRuleValueRepository extends DALUtils.mikroOrmBaseRepositor
     update: RepositoryTypes.UpdatePriceListRuleValueDTO
   }
 >(PriceListRuleValue) {
+  constructor(...args: any[]) {
+    // @ts-ignore
+    super(...arguments)
+  }
+
   async create(
     data: RepositoryTypes.CreatePriceListRuleValueDTO[],
     context: Context = {}
diff --git a/packages/pricing/src/repositories/price-list-rule.ts b/packages/pricing/src/repositories/price-list-rule.ts
index 2e0664fc78..481549f7ab 100644
--- a/packages/pricing/src/repositories/price-list-rule.ts
+++ b/packages/pricing/src/repositories/price-list-rule.ts
@@ -7,6 +7,11 @@ import { RepositoryTypes } from "@types"
 export class PriceListRuleRepository extends DALUtils.mikroOrmBaseRepositoryFactory(
   PriceListRule
 ) {
+  constructor(...args: any[]) {
+    // @ts-ignore
+    super(...arguments)
+  }
+
   async create(
     data: RepositoryTypes.CreatePriceListRuleDTO[],
     context: Context = {}
diff --git a/packages/pricing/src/repositories/price-list.ts b/packages/pricing/src/repositories/price-list.ts
index 6245fbb752..e1db5946df 100644
--- a/packages/pricing/src/repositories/price-list.ts
+++ b/packages/pricing/src/repositories/price-list.ts
@@ -7,6 +7,11 @@ import { RepositoryTypes } from "@types"
 export class PriceListRepository extends DALUtils.mikroOrmBaseRepositoryFactory(
   PriceList
 ) {
+  constructor(...args: any[]) {
+    // @ts-ignore
+    super(...arguments)
+  }
+
   async create(
     data: RepositoryTypes.CreatePriceListDTO[],
     context: Context = {}
diff --git a/packages/pricing/src/repositories/price-rule.ts b/packages/pricing/src/repositories/price-rule.ts
index 73ffe0a994..ce6d41ee30 100644
--- a/packages/pricing/src/repositories/price-rule.ts
+++ b/packages/pricing/src/repositories/price-rule.ts
@@ -10,6 +10,11 @@ export class PriceRuleRepository extends DALUtils.mikroOrmBaseRepositoryFactory<
     update: RepositoryTypes.UpdatePriceRuleDTO
   }
 >(PriceRule) {
+  constructor(...args: any[]) {
+    // @ts-ignore
+    super(...arguments)
+  }
+
   async create(
     data: RepositoryTypes.CreatePriceRuleDTO[],
     context: Context = {}
diff --git a/packages/pricing/src/repositories/price-set-money-amount-rules.ts b/packages/pricing/src/repositories/price-set-money-amount-rules.ts
index 1cec6d2c9a..8577254b9f 100644
--- a/packages/pricing/src/repositories/price-set-money-amount-rules.ts
+++ b/packages/pricing/src/repositories/price-set-money-amount-rules.ts
@@ -9,4 +9,9 @@ export class PriceSetMoneyAmountRulesRepository extends DALUtils.mikroOrmBaseRep
     create: RepositoryTypes.CreatePriceSetMoneyAmountRulesDTO
     update: RepositoryTypes.UpdatePriceSetMoneyAmountRulesDTO
   }
->(PriceSetMoneyAmountRules) {}
+>(PriceSetMoneyAmountRules) {
+  constructor(...args: any[]) {
+    // @ts-ignore
+    super(...arguments)
+  }
+}
diff --git a/packages/pricing/src/repositories/price-set-money-amount.ts b/packages/pricing/src/repositories/price-set-money-amount.ts
index 2c9a017d6e..dde772edc6 100644
--- a/packages/pricing/src/repositories/price-set-money-amount.ts
+++ b/packages/pricing/src/repositories/price-set-money-amount.ts
@@ -9,4 +9,9 @@ export class PriceSetMoneyAmountRepository extends DALUtils.mikroOrmBaseReposito
     create: RepositoryTypes.CreatePriceSetMoneyAmountDTO
     update: RepositoryTypes.UpdatePriceSetMoneyAmountDTO
   }
->(PriceSetMoneyAmount) {}
+>(PriceSetMoneyAmount) {
+  constructor(...args: any[]) {
+    // @ts-ignore
+    super(...arguments)
+  }
+}
diff --git a/packages/pricing/src/repositories/price-set-rule-type.ts b/packages/pricing/src/repositories/price-set-rule-type.ts
index 1dea5f21ad..9cffb54d7e 100644
--- a/packages/pricing/src/repositories/price-set-rule-type.ts
+++ b/packages/pricing/src/repositories/price-set-rule-type.ts
@@ -9,4 +9,9 @@ export class PriceSetRuleTypeRepository extends DALUtils.mikroOrmBaseRepositoryF
     create: RepositoryTypes.CreatePriceSetRuleTypeDTO
     update: RepositoryTypes.UpdatePriceSetRuleTypeDTO
   }
->(PriceSetRuleType) {}
+>(PriceSetRuleType) {
+  constructor(...args: any[]) {
+    // @ts-ignore
+    super(...arguments)
+  }
+}
diff --git a/packages/pricing/src/repositories/price-set.ts b/packages/pricing/src/repositories/price-set.ts
index 03984ca0e0..94cfe23065 100644
--- a/packages/pricing/src/repositories/price-set.ts
+++ b/packages/pricing/src/repositories/price-set.ts
@@ -9,4 +9,9 @@ export class PriceSetRepository extends DALUtils.mikroOrmBaseRepositoryFactory<
     create: RepositoryTypes.CreatePriceSetDTO
     update: RepositoryTypes.UpdatePriceSetDTO
   }
->(PriceSet) {}
+>(PriceSet) {
+  constructor(...args: any[]) {
+    // @ts-ignore
+    super(...arguments)
+  }
+}
diff --git a/packages/pricing/src/repositories/rule-type.ts b/packages/pricing/src/repositories/rule-type.ts
index 1873ad675d..21d9f3d4f1 100644
--- a/packages/pricing/src/repositories/rule-type.ts
+++ b/packages/pricing/src/repositories/rule-type.ts
@@ -8,4 +8,9 @@ export class RuleTypeRepository extends DALUtils.mikroOrmBaseRepositoryFactory<
     create: RepositoryTypes.CreateRuleTypeDTO
     update: RepositoryTypes.UpdateRuleTypeDTO
   }
->(RuleType) {}
+>(RuleType) {
+  constructor(...args: any[]) {
+    // @ts-ignore
+    super(...arguments)
+  }
+}
diff --git a/packages/product/src/repositories/product-collection.ts b/packages/product/src/repositories/product-collection.ts
index 9fcdb62d19..6a8310e0f4 100644
--- a/packages/product/src/repositories/product-collection.ts
+++ b/packages/product/src/repositories/product-collection.ts
@@ -14,6 +14,11 @@ type CreateProductCollection = ProductTypes.CreateProductCollectionDTO & {
 export class ProductCollectionRepository extends DALUtils.mikroOrmBaseRepositoryFactory(
   ProductCollection
 ) {
+  constructor(...args: any[]) {
+    // @ts-ignore
+    super(...arguments)
+  }
+
   async create(
     data: CreateProductCollection[],
     context: Context = {}
diff --git a/packages/product/src/repositories/product-image.ts b/packages/product/src/repositories/product-image.ts
index de12c58c04..5dc1799b1c 100644
--- a/packages/product/src/repositories/product-image.ts
+++ b/packages/product/src/repositories/product-image.ts
@@ -7,6 +7,11 @@ import { DALUtils } from "@medusajs/utils"
 export class ProductImageRepository extends DALUtils.mikroOrmBaseRepositoryFactory(
   Image
 ) {
+  constructor(...args: any[]) {
+    // @ts-ignore
+    super(...arguments)
+  }
+
   async upsert(urls: string[], context: Context = {}): Promise<Image[]> {
     const manager = this.getActiveManager<SqlEntityManager>(context)
 
diff --git a/packages/product/src/repositories/product-option-value.ts b/packages/product/src/repositories/product-option-value.ts
index 219764cd35..2b29297430 100644
--- a/packages/product/src/repositories/product-option-value.ts
+++ b/packages/product/src/repositories/product-option-value.ts
@@ -11,6 +11,11 @@ import { SqlEntityManager } from "@mikro-orm/postgresql"
 export class ProductOptionValueRepository extends DALUtils.mikroOrmBaseRepositoryFactory(
   ProductOptionValue
 ) {
+  constructor(...args: any[]) {
+    // @ts-ignore
+    super(...arguments)
+  }
+
   async upsert(
     optionValues: (UpdateProductOptionValueDTO | CreateProductOptionValueDTO)[],
     context: Context = {}
diff --git a/packages/product/src/repositories/product-option.ts b/packages/product/src/repositories/product-option.ts
index a51f9260fb..fc4616acd0 100644
--- a/packages/product/src/repositories/product-option.ts
+++ b/packages/product/src/repositories/product-option.ts
@@ -10,6 +10,11 @@ export class ProductOptionRepository extends DALUtils.mikroOrmBaseRepositoryFact
     update: ProductTypes.UpdateProductOptionDTO
   }
 >(ProductOption) {
+  constructor(...args: any[]) {
+    // @ts-ignore
+    super(...arguments)
+  }
+
   async create(
     data: ProductTypes.CreateProductOptionDTO[],
     context: Context = {}
diff --git a/packages/product/src/repositories/product-tag.ts b/packages/product/src/repositories/product-tag.ts
index 69dfb03ea7..e3eae1543c 100644
--- a/packages/product/src/repositories/product-tag.ts
+++ b/packages/product/src/repositories/product-tag.ts
@@ -15,6 +15,11 @@ export class ProductTagRepository extends DALUtils.mikroOrmBaseRepositoryFactory
     update: UpdateProductTagDTO
   }
 >(ProductTag) {
+  constructor(...args: any[]) {
+    // @ts-ignore
+    super(...arguments)
+  }
+
   async upsert(
     tags: UpsertProductTagDTO[],
     context: Context = {}
diff --git a/packages/product/src/repositories/product-type.ts b/packages/product/src/repositories/product-type.ts
index 082a926bcf..352ff1ace8 100644
--- a/packages/product/src/repositories/product-type.ts
+++ b/packages/product/src/repositories/product-type.ts
@@ -14,6 +14,11 @@ export class ProductTypeRepository extends DALUtils.mikroOrmBaseRepositoryFactor
     update: UpdateProductTypeDTO
   }
 >(ProductType) {
+  constructor(...args: any[]) {
+    // @ts-ignore
+    super(...arguments)
+  }
+
   async upsert(
     types: CreateProductTypeDTO[],
     context: Context = {}
diff --git a/packages/product/src/repositories/product-variant.ts b/packages/product/src/repositories/product-variant.ts
index 3e7824e9c6..f792a8e3be 100644
--- a/packages/product/src/repositories/product-variant.ts
+++ b/packages/product/src/repositories/product-variant.ts
@@ -14,4 +14,9 @@ export class ProductVariantRepository extends DALUtils.mikroOrmBaseRepositoryFac
       "id"
     >
   }
->(ProductVariant) {}
+>(ProductVariant) {
+  constructor(...args: any[]) {
+    // @ts-ignore
+    super(...arguments)
+  }
+}
diff --git a/packages/product/src/repositories/product.ts b/packages/product/src/repositories/product.ts
index 855477db87..833c61e9d5 100644
--- a/packages/product/src/repositories/product.ts
+++ b/packages/product/src/repositories/product.ts
@@ -24,6 +24,11 @@ export class ProductRepository extends DALUtils.mikroOrmBaseRepositoryFactory<
     create: WithRequiredProperty<ProductTypes.CreateProductOnlyDTO, "status">
   }
 >(Product) {
+  constructor(...args: any[]) {
+    // @ts-ignore
+    super(...arguments)
+  }
+
   async find(
     findOptions: DAL.FindOptions<Product & { q?: string }> = { where: {} },
     context: Context = {}
diff --git a/packages/promotion/src/repositories/application-method.ts b/packages/promotion/src/repositories/application-method.ts
index f2d7a60517..fd666d995b 100644
--- a/packages/promotion/src/repositories/application-method.ts
+++ b/packages/promotion/src/repositories/application-method.ts
@@ -8,4 +8,9 @@ export class ApplicationMethodRepository extends DALUtils.mikroOrmBaseRepository
     create: CreateApplicationMethodDTO
     update: UpdateApplicationMethodDTO
   }
->(ApplicationMethod) {}
+>(ApplicationMethod) {
+  constructor(...args: any[]) {
+    // @ts-ignore
+    super(...arguments)
+  }
+}
diff --git a/packages/promotion/src/repositories/promotion-rule-value.ts b/packages/promotion/src/repositories/promotion-rule-value.ts
index aa3868e5bf..7587fa295c 100644
--- a/packages/promotion/src/repositories/promotion-rule-value.ts
+++ b/packages/promotion/src/repositories/promotion-rule-value.ts
@@ -11,4 +11,9 @@ export class PromotionRuleValueRepository extends DALUtils.mikroOrmBaseRepositor
     create: CreatePromotionRuleValueDTO
     update: UpdatePromotionRuleValueDTO
   }
->(PromotionRuleValue) {}
+>(PromotionRuleValue) {
+  constructor(...args: any[]) {
+    // @ts-ignore
+    super(...arguments)
+  }
+}
diff --git a/packages/promotion/src/repositories/promotion-rule.ts b/packages/promotion/src/repositories/promotion-rule.ts
index d80c92c9f0..aceb5d33dd 100644
--- a/packages/promotion/src/repositories/promotion-rule.ts
+++ b/packages/promotion/src/repositories/promotion-rule.ts
@@ -8,4 +8,9 @@ export class PromotionRuleRepository extends DALUtils.mikroOrmBaseRepositoryFact
     create: CreatePromotionRuleDTO
     update: UpdatePromotionRuleDTO
   }
->(PromotionRule) {}
+>(PromotionRule) {
+  constructor(...args: any[]) {
+    // @ts-ignore
+    super(...arguments)
+  }
+}
diff --git a/packages/promotion/src/repositories/promotion.ts b/packages/promotion/src/repositories/promotion.ts
index 0df0002f02..c6732c74ba 100644
--- a/packages/promotion/src/repositories/promotion.ts
+++ b/packages/promotion/src/repositories/promotion.ts
@@ -8,4 +8,9 @@ export class PromotionRepository extends DALUtils.mikroOrmBaseRepositoryFactory<
     create: CreatePromotionDTO
     Update: UpdatePromotionDTO
   }
->(Promotion) {}
+>(Promotion) {
+  constructor(...args: any[]) {
+    // @ts-ignore
+    super(...arguments)
+  }
+}
diff --git a/packages/utils/src/dal/mikro-orm/mikro-orm-repository.ts b/packages/utils/src/dal/mikro-orm/mikro-orm-repository.ts
index 84c8b437f2..da3f18819c 100644
--- a/packages/utils/src/dal/mikro-orm/mikro-orm-repository.ts
+++ b/packages/utils/src/dal/mikro-orm/mikro-orm-repository.ts
@@ -7,7 +7,6 @@ import {
 import {
   EntityManager,
   EntitySchema,
-  FilterQuery,
   LoadStrategy,
   RequiredEntityData,
 } from "@mikro-orm/core"
@@ -17,9 +16,9 @@ import {
   EntityName,
   FilterQuery as MikroFilterQuery,
 } from "@mikro-orm/core/typings"
-import { MedusaError, arrayDifference, isString } from "../../common"
+import { isString, MedusaError } from "../../common"
 import { MedusaContext } from "../../decorators"
-import { InjectTransactionManager, buildQuery } from "../../modules-sdk"
+import { buildQuery, InjectTransactionManager } from "../../modules-sdk"
 import {
   getSoftDeletedCascadedEntitiesIdsMappedBy,
   transactionWrapper,
@@ -77,10 +76,11 @@ export class MikroOrmBase<T = any> {
 export class MikroOrmBaseRepository<
   T extends object = object
 > extends MikroOrmBase<T> {
-  constructor() {
+  constructor(...args: any[]) {
     // @ts-ignore
     super(...arguments)
   }
+
   create(data: unknown[], context?: Context): Promise<T[]> {
     throw new Error("Method not implemented.")
   }
@@ -89,7 +89,7 @@ export class MikroOrmBaseRepository<
     throw new Error("Method not implemented.")
   }
 
-  delete(ids: string[], context?: Context): Promise<void> {
+  delete(ids: string[] | object[], context?: Context): Promise<void> {
     throw new Error("Method not implemented.")
   }
 
@@ -227,11 +227,25 @@ export function mikroOrmBaseRepositoryFactory<
   TDTos extends { [K in DtoBasedMutationMethods]?: any } = {
     [K in DtoBasedMutationMethods]?: any
   }
->(
-  entity: EntityClass<T> | EntitySchema<T> | string,
-  primaryKey: string = "id"
-) {
+>(entity: EntityClass<T> | EntitySchema<T>) {
   class MikroOrmAbstractBaseRepository_ extends MikroOrmBaseRepository<T> {
+    // @ts-ignore
+    constructor(...args: any[]) {
+      // @ts-ignore
+      super(...arguments)
+    }
+
+    static buildUniqueCompositeKeyValue(keys: string[], data: object) {
+      return keys.map((k) => data[k]).join("_")
+    }
+
+    static retrievePrimaryKeys(entity: EntityClass<T> | EntitySchema<T>) {
+      return (
+        (entity as EntitySchema<T>).meta?.primaryKeys ??
+        (entity as EntityClass<T>).prototype.__meta.primaryKeys
+      )
+    }
+
     async create(data: TDTos["create"][], context?: Context): Promise<T[]> {
       const manager = this.getActiveManager<EntityManager>(context)
 
@@ -250,42 +264,71 @@ export function mikroOrmBaseRepositoryFactory<
     async update(data: TDTos["update"][], context?: Context): Promise<T[]> {
       const manager = this.getActiveManager<EntityManager>(context)
 
-      const primaryKeyValues: string[] = data.map((data_) => data_[primaryKey])
-      const existingEntities = await this.find(
-        {
-          where: {
-            [primaryKey]: {
-              $in: primaryKeyValues,
-            },
-          },
-        } as DAL.FindOptions<T>,
-        context
+      const primaryKeys =
+        MikroOrmAbstractBaseRepository_.retrievePrimaryKeys(entity)
+
+      let primaryKeysCriteria: { [key: string]: any }[] = []
+      if (primaryKeys.length === 1) {
+        primaryKeysCriteria.push({
+          [primaryKeys[0]]: data.map((d) => d[primaryKeys[0]]),
+        })
+      } else {
+        primaryKeysCriteria = data.map((d) => ({
+          $and: primaryKeys.map((key) => ({ [key]: d[key] })),
+        }))
+      }
+
+      const allEntities = await Promise.all(
+        primaryKeysCriteria.map(
+          async (criteria) =>
+            await this.find({ where: criteria } as DAL.FindOptions<T>, context)
+        )
       )
 
-      const missingEntities = arrayDifference(
-        data.map((d) => d[primaryKey]),
-        existingEntities.map((d: any) => d[primaryKey])
-      )
+      const existingEntities = allEntities.flat()
+
+      const existingEntitiesMap = new Map<string, T>()
+      existingEntities.forEach((entity) => {
+        if (entity) {
+          const key =
+            MikroOrmAbstractBaseRepository_.buildUniqueCompositeKeyValue(
+              primaryKeys,
+              entity
+            )
+          existingEntitiesMap.set(key, entity)
+        }
+      })
+
+      const missingEntities = data.filter((data_) => {
+        const key =
+          MikroOrmAbstractBaseRepository_.buildUniqueCompositeKeyValue(
+            primaryKeys,
+            data_
+          )
+        return !existingEntitiesMap.has(key)
+      })
 
       if (missingEntities.length) {
         const entityName = (entity as EntityClass<T>).name ?? entity
+        const missingEntitiesKeys = data.map((data_) =>
+          primaryKeys.map((key) => data_[key]).join(", ")
+        )
         throw new MedusaError(
           MedusaError.Types.NOT_FOUND,
-          `${entityName} with ${[primaryKey]} "${missingEntities.join(
+          `${entityName} with ${primaryKeys.join(
             ", "
-          )}" not found`
+          )} "${missingEntitiesKeys.join(", ")}" not found`
         )
       }
 
-      const existingEntitiesMap = new Map(
-        existingEntities.map<[string, T]>((entity_: any) => [
-          entity_[primaryKey],
-          entity_,
-        ])
-      )
-
       const entities = data.map((data_) => {
-        const existingEntity = existingEntitiesMap.get(data_[primaryKey])!
+        const key =
+          MikroOrmAbstractBaseRepository_.buildUniqueCompositeKeyValue(
+            primaryKeys,
+            data_
+          )
+        const existingEntity = existingEntitiesMap.get(key)!
+
         return manager.assign(existingEntity, data_ as RequiredEntityData<T>)
       })
 
@@ -294,13 +337,41 @@ export function mikroOrmBaseRepositoryFactory<
       return entities
     }
 
-    async delete(primaryKeyValues: string[], context?: Context): Promise<void> {
+    async delete(
+      primaryKeyValues: string[] | object[],
+      context?: Context
+    ): Promise<void> {
       const manager = this.getActiveManager<EntityManager>(context)
 
-      await manager.nativeDelete<T>(
-        entity as EntityName<T>,
-        { [primaryKey]: { $in: primaryKeyValues } } as unknown as FilterQuery<T>
-      )
+      const primaryKeys =
+        MikroOrmAbstractBaseRepository_.retrievePrimaryKeys(entity)
+
+      let deletionCriteria
+      if (primaryKeys.length > 1) {
+        deletionCriteria = {
+          $or: primaryKeyValues.map((compositeKeyValue) => {
+            const keys = Object.keys(compositeKeyValue)
+            if (!primaryKeys.every((k) => keys.includes(k))) {
+              throw new MedusaError(
+                MedusaError.Types.INVALID_DATA,
+                `Composite key must contain all primary key fields: ${primaryKeys.join(
+                  ", "
+                )}. Found: ${keys}`
+              )
+            }
+
+            const criteria: { [key: string]: any } = {}
+            for (const key of primaryKeys) {
+              criteria[key] = compositeKeyValue[key]
+            }
+            return criteria
+          }),
+        }
+      } else {
+        deletionCriteria = { [primaryKeys[0]]: { $in: primaryKeyValues } }
+      }
+
+      await manager.nativeDelete<T>(entity as EntityName<T>, deletionCriteria)
     }
 
     async find(options?: DAL.FindOptions<T>, context?: Context): Promise<T[]> {