diff --git a/.aspect/rules/external_repository_action_cache/npm_translate_lock_LTE4Nzc1MDcwNjU= b/.aspect/rules/external_repository_action_cache/npm_translate_lock_LTE4Nzc1MDcwNjU=
index 734bec640..190a6a18d 100755
--- a/.aspect/rules/external_repository_action_cache/npm_translate_lock_LTE4Nzc1MDcwNjU=
+++ b/.aspect/rules/external_repository_action_cache/npm_translate_lock_LTE4Nzc1MDcwNjU=
@@ -2,9 +2,9 @@
 # Input hashes for repository rule npm_translate_lock(name = "npm", pnpm_lock = "//:pnpm-lock.yaml").
 # This file should be checked into version control along with the pnpm-lock.yaml file.
 .npmrc=-2065072158
-pnpm-lock.yaml=-2123305961
+pnpm-lock.yaml=-1324340320
 examples/npm_deps/patches/meaning-of-life@1.0.0-pnpm.patch=-442666336
-package.json=-1057425123
+package.json=965846805
 pnpm-workspace.yaml=1536402859
 examples/js_binary/package.json=-41174383
 examples/macro/package.json=857146175
@@ -17,8 +17,8 @@ js/private/coverage/bundle/package.json=-1543718929
 js/private/image/package.json=-266007263
 js/private/test/image/package.json=1295393035
 js/private/worker/src/package.json=-715289696
-npm/private/test/package.json=1920219401
+npm/private/test/package.json=1424344949
 npm/private/test/vendored/lodash-4.17.21.tgz=-1206623349
-npm/private/test/npm_package/package.json=-1377103079
+npm/private/test/npm_package/package.json=-1991705133
 npm/private/test/vendored/is-odd/package.json=1041695223
 npm/private/test/vendored/semver-max/package.json=578664053
diff --git a/e2e/pnpm_workspace_deps/.aspect/rules/external_repository_action_cache/npm_translate_lock_LTE4Nzc1MDcwNjU= b/e2e/pnpm_workspace_deps/.aspect/rules/external_repository_action_cache/npm_translate_lock_LTE4Nzc1MDcwNjU=
index 09937d840..905668881 100755
--- a/e2e/pnpm_workspace_deps/.aspect/rules/external_repository_action_cache/npm_translate_lock_LTE4Nzc1MDcwNjU=
+++ b/e2e/pnpm_workspace_deps/.aspect/rules/external_repository_action_cache/npm_translate_lock_LTE4Nzc1MDcwNjU=
@@ -1,7 +1,9 @@
+# @generated
 # Input hashes for repository rule npm_translate_lock(name = "npm", pnpm_lock = "//:pnpm-lock.yaml").
 # This file should be checked into version control along with the pnpm-lock.yaml file.
-pnpm-lock.yaml=-1808949182
+pnpm-lock.yaml=-1199344695
 package.json=959251505
-pnpm-workspace.yaml=1047324817
+pnpm-workspace.yaml=-2026278039
 lib/package.json=-275126300
-tests/package.json=-641014960
+lib-dupes/package.json=-725174835
+tests/package.json=-1421585247
diff --git a/e2e/pnpm_workspace_deps/.bazelignore b/e2e/pnpm_workspace_deps/.bazelignore
index e45690809..79fa086c2 100644
--- a/e2e/pnpm_workspace_deps/.bazelignore
+++ b/e2e/pnpm_workspace_deps/.bazelignore
@@ -1,3 +1,4 @@
 node_modules/
 lib/node_modules
+lib-dupes/node_modules
 tests/node_modules
\ No newline at end of file
diff --git a/e2e/pnpm_workspace_deps/MODULE.bazel b/e2e/pnpm_workspace_deps/MODULE.bazel
index 1a6c4c971..264ddc99d 100644
--- a/e2e/pnpm_workspace_deps/MODULE.bazel
+++ b/e2e/pnpm_workspace_deps/MODULE.bazel
@@ -17,6 +17,7 @@ npm.npm_translate_lock(
         "//:package.json",
         "//:pnpm-workspace.yaml",
         "//lib:package.json",
+        "//lib-dupes:package.json",
         "//tests:package.json",
     ],
     pnpm_lock = "//:pnpm-lock.yaml",
diff --git a/e2e/pnpm_workspace_deps/WORKSPACE b/e2e/pnpm_workspace_deps/WORKSPACE
index 20fe0afb2..e43c4a5b9 100644
--- a/e2e/pnpm_workspace_deps/WORKSPACE
+++ b/e2e/pnpm_workspace_deps/WORKSPACE
@@ -22,6 +22,7 @@ npm_translate_lock(
         "//:package.json",
         "//:pnpm-workspace.yaml",
         "//lib:package.json",
+        "//lib-dupes:package.json",
         "//tests:package.json",
     ],
     pnpm_lock = "//:pnpm-lock.yaml",
diff --git a/e2e/pnpm_workspace_deps/lib-dupes/BUILD.bazel b/e2e/pnpm_workspace_deps/lib-dupes/BUILD.bazel
new file mode 100644
index 000000000..882665afd
--- /dev/null
+++ b/e2e/pnpm_workspace_deps/lib-dupes/BUILD.bazel
@@ -0,0 +1,27 @@
+load("@aspect_rules_js//npm:defs.bzl", "npm_package")
+load("@aspect_rules_js//js:defs.bzl", "js_library")
+load("@npm//:defs.bzl", "npm_link_all_packages")
+
+npm_link_all_packages(name = "node_modules")
+
+# A library with 2 aliases to one simple dependency (package with no dependencies)
+js_library(
+    name = "js_lib_dupes",
+    srcs = ["index.js"],
+    data = [
+        # Two versions of the same package (via aliases), see https://github.com/aspect-build/rules_js/issues/1110
+        ":node_modules/@aspect-test/c",
+        ":node_modules/@aspect-test/c1",
+    ],
+    visibility = ["//visibility:public"],
+)
+
+# Exposed via npm_package()
+npm_package(
+    name = "lib-dupes",
+    srcs = [
+        "package.json",
+        ":js_lib_dupes",
+    ],
+    visibility = ["//visibility:public"],
+)
diff --git a/e2e/pnpm_workspace_deps/lib-dupes/index.js b/e2e/pnpm_workspace_deps/lib-dupes/index.js
new file mode 100644
index 000000000..b2a0c2a03
--- /dev/null
+++ b/e2e/pnpm_workspace_deps/lib-dupes/index.js
@@ -0,0 +1,5 @@
+// Two versions of the same package referenced throught aliases, see https://github.com/aspect-build/rules_js/issues/1110
+module.exports = {
+    importDep: () => require('@aspect-test/c'),
+    importDupeDep: () => require('@aspect-test/c1'),
+}
diff --git a/e2e/pnpm_workspace_deps/lib-dupes/package.json b/e2e/pnpm_workspace_deps/lib-dupes/package.json
new file mode 100644
index 000000000..dbfd9304e
--- /dev/null
+++ b/e2e/pnpm_workspace_deps/lib-dupes/package.json
@@ -0,0 +1,8 @@
+{
+    "name": "@lib/test-dupes",
+    "private": true,
+    "dependencies": {
+        "@aspect-test/c": "2.0.0",
+        "@aspect-test/c1": "npm:@aspect-test/c@1.0.0"
+    }
+}
diff --git a/e2e/pnpm_workspace_deps/pnpm-lock.yaml b/e2e/pnpm_workspace_deps/pnpm-lock.yaml
index 3eeda505f..6b1577d6d 100644
--- a/e2e/pnpm_workspace_deps/pnpm-lock.yaml
+++ b/e2e/pnpm_workspace_deps/pnpm-lock.yaml
@@ -18,14 +18,38 @@ importers:
         specifier: 1.0.0
         version: 1.0.0
 
+  lib-dupes:
+    dependencies:
+      '@aspect-test/c':
+        specifier: 2.0.0
+        version: 2.0.0
+      '@aspect-test/c1':
+        specifier: npm:@aspect-test/c@1.0.0
+        version: /@aspect-test/c@1.0.0
+
   tests:
     dependencies:
       '@lib/test':
         specifier: workspace:*
         version: link:../lib
+      '@lib/test-dupes':
+        specifier: workspace:*
+        version: link:../lib-dupes
 
 packages:
 
+  /@aspect-test/c@1.0.0:
+    resolution: {integrity: sha512-UorLD4TFr9CWFeYbUd5etaxSo201fYEFR+rSxXytfzefX41EWCBabsXhdhvXjK6v/HRuo1y1I1NiW2P3/bKJeA==}
+    hasBin: true
+    requiresBuild: true
+    dev: false
+
+  /@aspect-test/c@2.0.0:
+    resolution: {integrity: sha512-vRuHi/8zxZ+IRGdgdX4VoMNFZrR9UqO87yQx61IGIkjgV7QcKUeu5jfvIE3Mr0WNQeMdO1JpyTx1UUpsE73iug==}
+    hasBin: true
+    requiresBuild: true
+    dev: false
+
   /@aspect-test/e@1.0.0:
     resolution: {integrity: sha512-GyAxHYKN650db+xnimHnL2LPz65ilmQsVhCasWA7drDNQn/rfmPiEVMzjRiS7m46scXIERaBmiJMzYDf0bIUbA==}
     hasBin: true
diff --git a/e2e/pnpm_workspace_deps/pnpm-workspace.yaml b/e2e/pnpm_workspace_deps/pnpm-workspace.yaml
index d7b2c95aa..482b6ae28 100644
--- a/e2e/pnpm_workspace_deps/pnpm-workspace.yaml
+++ b/e2e/pnpm_workspace_deps/pnpm-workspace.yaml
@@ -1,3 +1,4 @@
 packages:
     - lib
+    - lib-dupes
     - tests
diff --git a/e2e/pnpm_workspace_deps/tests/BUILD.bazel b/e2e/pnpm_workspace_deps/tests/BUILD.bazel
index a545b5ef1..b4f22176f 100644
--- a/e2e/pnpm_workspace_deps/tests/BUILD.bazel
+++ b/e2e/pnpm_workspace_deps/tests/BUILD.bazel
@@ -20,3 +20,11 @@ js_test(
     ],
     entry_point = "test_pkg_deps_linked.js",
 )
+
+js_test(
+    name = "dupes",
+    data = [
+        ":node_modules/@lib/test-dupes",
+    ],
+    entry_point = "test_pkg_dupe_deps_linked.js",
+)
diff --git a/e2e/pnpm_workspace_deps/tests/package.json b/e2e/pnpm_workspace_deps/tests/package.json
index b729c6057..b9c0c03cd 100644
--- a/e2e/pnpm_workspace_deps/tests/package.json
+++ b/e2e/pnpm_workspace_deps/tests/package.json
@@ -1,6 +1,7 @@
 {
     "name": "tests",
     "dependencies": {
-        "@lib/test": "workspace:*"
+        "@lib/test": "workspace:*",
+        "@lib/test-dupes": "workspace:*"
     }
 }
diff --git a/e2e/pnpm_workspace_deps/tests/test_pkg_dupe_deps_linked.js b/e2e/pnpm_workspace_deps/tests/test_pkg_dupe_deps_linked.js
new file mode 100644
index 000000000..bd3873a82
--- /dev/null
+++ b/e2e/pnpm_workspace_deps/tests/test_pkg_dupe_deps_linked.js
@@ -0,0 +1,7 @@
+const testLibDupes = require('@lib/test-dupes')
+
+console.log('loaded dependency', testLibDupes.importDep().id())
+console.log(
+    'loaded duplicate aliased dependency',
+    testLibDupes.importDupeDep().id()
+)
diff --git a/npm/private/npm_package_store.bzl b/npm/private/npm_package_store.bzl
index d4bc42775..785201c01 100644
--- a/npm/private/npm_package_store.bzl
+++ b/npm/private/npm_package_store.bzl
@@ -178,7 +178,7 @@ def _impl(ctx):
     transitive_files = []
     direct_ref_deps = {}
 
-    npm_package_store_deps = ctx.attr.src[NpmPackageInfo].npm_package_store_deps.to_list() if ctx.attr.src else []
+    npm_package_store_deps = []
 
     if ctx.attr.src:
         # output the package as a TreeArtifact to its virtual store location
@@ -206,14 +206,7 @@ def _impl(ctx):
                 verbose = ctx.attr.verbose,
             )
 
-        for store in npm_package_store_deps:
-            dep_package = store.package
-            dep_virtual_store_directory = store.virtual_store_directory
-
-            # "node_modules/{virtual_store_root}/{virtual_store_name}/node_modules/{package}"
-            dep_symlink_path = paths.join("node_modules", utils.virtual_store_root, virtual_store_name, "node_modules", dep_package)
-            transitive_files.extend(utils.make_symlink(ctx, dep_symlink_path, dep_virtual_store_directory))
-
+        linked_virtual_store_directories = []
         for dep, _dep_aliases in ctx.attr.deps.items():
             # symlink the package's direct deps to its virtual store location
             if dep[NpmPackageStoreInfo].root_package != ctx.label.package:
@@ -224,16 +217,29 @@ deps of npm_package_store must be in the same package.""" % (ctx.label.package,
             dep_aliases = _dep_aliases.split(",") if _dep_aliases else [dep_package]
             dep_virtual_store_directory = dep[NpmPackageStoreInfo].virtual_store_directory
             if dep_virtual_store_directory:
+                linked_virtual_store_directories.append(dep_virtual_store_directory)
                 for dep_alias in dep_aliases:
                     # "node_modules/{virtual_store_root}/{virtual_store_name}/node_modules/{package}"
                     dep_symlink_path = paths.join("node_modules", utils.virtual_store_root, virtual_store_name, "node_modules", dep_alias)
                     transitive_files.extend(utils.make_symlink(ctx, dep_symlink_path, dep_virtual_store_directory))
             else:
                 # this is a ref npm_link_package, a downstream terminal npm_link_package
-                # for this npm depedency will create the dep symlinks for this dep;
+                # for this npm dependency will create the dep symlinks for this dep;
                 # this pattern is used to break circular dependencies between 3rd
                 # party npm deps; it is not recommended for 1st party deps
                 direct_ref_deps[dep] = dep_aliases
+
+        for store in ctx.attr.src[NpmPackageInfo].npm_package_store_deps.to_list():
+            dep_package = store.package
+            dep_virtual_store_directory = store.virtual_store_directory
+
+            # only link npm package store deps from NpmPackageInfo if they have _not_ already been linked directly
+            # from deps; fixes https://github.com/aspect-build/rules_js/issues/1110.
+            if dep_virtual_store_directory not in linked_virtual_store_directories:
+                # "node_modules/{virtual_store_root}/{virtual_store_name}/node_modules/{package}"
+                dep_symlink_path = paths.join("node_modules", utils.virtual_store_root, virtual_store_name, "node_modules", dep_package)
+                transitive_files.extend(utils.make_symlink(ctx, dep_symlink_path, dep_virtual_store_directory))
+                npm_package_store_deps.append(store)
     else:
         # if ctx.attr.src is _not_ set and ctx.attr.deps is, this is a terminal
         # package with deps being the transitive closure of deps;
diff --git a/npm/private/test/BUILD.bazel b/npm/private/test/BUILD.bazel
index 50c679625..263ea81d5 100644
--- a/npm/private/test/BUILD.bazel
+++ b/npm/private/test/BUILD.bazel
@@ -62,6 +62,7 @@ build_test(
         ":node_modules/json-stable-stringify",
         ":node_modules/lodash",  # lodash is brought in as a vendored .tgz file: vendored/lodash-4.17.21.tgz
         ":node_modules/node-gyp",
+        ":node_modules/test-npm_package",
         ":node_modules/plotly.js",
         ":node_modules/protoc-gen-grpc",
         ":node_modules/regl",
diff --git a/npm/private/test/npm_package/BUILD.bazel b/npm/private/test/npm_package/BUILD.bazel
index 86481201b..d6663901b 100644
--- a/npm/private/test/npm_package/BUILD.bazel
+++ b/npm/private/test/npm_package/BUILD.bazel
@@ -13,19 +13,22 @@ js_library(
         ":package.json",
     ],
     deps = [
-        # node_modules deps should be excluded from the contents of the npm_package
+        # 1. node_modules deps should be excluded from the contents of the npm_package
+        # 2. include 2 versions of chalk to test cases such as https://github.com/aspect-build/rules_js/issues/1110
         ":node_modules/chalk",
+        "//:node_modules/chalk",
     ],
 )
 
 npm_package(
-    name = "pkg_a",
+    name = "npm_package",
     srcs = [":lib_a"],
     include_runfiles = False,
+    visibility = ["//visibility:public"],
 )
 
 copy_to_directory(
-    name = "expected_pkg_a",
+    name = "expected_npm_package",
     srcs = [
         "index.js",
         ":package.json",
@@ -34,6 +37,6 @@ copy_to_directory(
 
 diff_test(
     name = "test",
-    file1 = ":pkg_a",
-    file2 = ":expected_pkg_a",
+    file1 = ":npm_package",
+    file2 = ":expected_npm_package",
 )
diff --git a/npm/private/test/npm_package/index.js b/npm/private/test/npm_package/index.js
index 4f6a8655b..ebc924939 100644
--- a/npm/private/test/npm_package/index.js
+++ b/npm/private/test/npm_package/index.js
@@ -1,2 +1,5 @@
+// Import two versions (via aliases) of the same package, see https://github.com/aspect-build/rules_js/issues/1110
 const chalk = require('chalk')
-console.log(chalk.italic.green('42'))
+const chalkAlt = require('chalk-alt')
+
+console.log(chalk.italic.green('Answer:'), chalkAlt.bold.red('42'))
diff --git a/npm/private/test/npm_package/package.json b/npm/private/test/npm_package/package.json
index b14f7db0b..229de8f34 100644
--- a/npm/private/test/npm_package/package.json
+++ b/npm/private/test/npm_package/package.json
@@ -1,6 +1,8 @@
 {
+    "name": "test-npm_package",
     "private": true,
     "dependencies": {
-        "chalk": "5.0.1"
+        "chalk": "5.0.1",
+        "chalk-alt": "npm:chalk@5.1.1"
     }
 }
diff --git a/npm/private/test/package.json b/npm/private/test/package.json
index 5c8b773c7..33dc01a61 100644
--- a/npm/private/test/package.json
+++ b/npm/private/test/package.json
@@ -23,6 +23,7 @@
         "syncpack": "git+https://github.com/JamieMason/syncpack.git#c245af8ea73ce3345d92bbda6c684092a841e262",
         "typescript": "*",
         "unused": "latest",
+        "test-npm_package": "workspace:*",
         "webpack-bundle-analyzer": "4.5.0"
     }
 }
diff --git a/npm/private/test/repositories_checked.bzl b/npm/private/test/repositories_checked.bzl
index 90eb9c62c..9c8f62ace 100644
--- a/npm/private/test/repositories_checked.bzl
+++ b/npm/private/test/repositories_checked.bzl
@@ -6308,6 +6308,25 @@ def npm_repositories():
         },
     )
 
+    npm_import(
+        name = "npm__chalk__5.1.1",
+        root_package = "",
+        link_workspace = "",
+        link_packages = {
+            "": ["chalk"],
+            "npm/private/test/npm_package": ["chalk-alt"],
+        },
+        package = "chalk",
+        version = "5.1.1",
+        url = "https://registry.npmjs.org/chalk/-/chalk-5.1.1.tgz",
+        npm_translate_lock_repo = "npm",
+        generate_bzl_library_targets = True,
+        integrity = "sha512-OItMegkSDU3P7OJRWBbNRsQsL8SzgwlIGXSZRVfHCLBYrDgzYDuozwDMwvEDpiZdjr50tdOTbTzuubirtEozsg==",
+        transitive_closure = {
+            "chalk": ["5.1.1"],
+        },
+    )
+
     npm_import(
         name = "npm__charenc__0.0.2",
         root_package = "",
diff --git a/package.json b/package.json
index f6ae75023..b1f7cf110 100644
--- a/package.json
+++ b/package.json
@@ -2,6 +2,7 @@
     "private": true,
     "devDependencies": {
         "@types/node": "16.18.11",
+        "chalk": "5.1.1",
         "inline-fixtures": "1.1.0",
         "jsonpath-plus": "7.2.0",
         "typescript": "4.9.5"
diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml
index 69ce104a8..a696a9d2b 100644
--- a/pnpm-lock.yaml
+++ b/pnpm-lock.yaml
@@ -23,6 +23,9 @@ importers:
       '@types/node':
         specifier: 16.18.11
         version: registry.npmjs.org/@types/node@16.18.11
+      chalk:
+        specifier: 5.1.1
+        version: 5.1.1
       inline-fixtures:
         specifier: 1.1.0
         version: 1.1.0
@@ -303,6 +306,9 @@ importers:
       syncpack:
         specifier: git+https://github.com/JamieMason/syncpack.git#c245af8ea73ce3345d92bbda6c684092a841e262
         version: github.com/JamieMason/syncpack/c245af8ea73ce3345d92bbda6c684092a841e262
+      test-npm_package:
+        specifier: workspace:*
+        version: link:npm_package
       typescript:
         specifier: '*'
         version: 4.9.5
@@ -318,6 +324,9 @@ importers:
       chalk:
         specifier: 5.0.1
         version: 5.0.1
+      chalk-alt:
+        specifier: npm:chalk@5.1.1
+        version: /chalk@5.1.1
 
 packages:
 
@@ -1995,6 +2004,10 @@ packages:
     engines: {node: ^12.17.0 || ^14.13 || >=16.0.0}
     dev: false
 
+  /chalk@5.1.1:
+    resolution: {integrity: sha512-OItMegkSDU3P7OJRWBbNRsQsL8SzgwlIGXSZRVfHCLBYrDgzYDuozwDMwvEDpiZdjr50tdOTbTzuubirtEozsg==}
+    engines: {node: ^12.17.0 || ^14.13 || >=16.0.0}
+
   /charenc@0.0.2:
     resolution: {integrity: sha512-yrLQ/yVUFXkzg7EDQsPieE/53+0RlaWTs+wBrvW36cyilJ2SaDWfl4Yj7MtLTXleV9uEKefbAGUPv2/iWSooRA==}
     dev: true