diff --git a/.changeset/polite-houses-design.md b/.changeset/polite-houses-design.md
new file mode 100644
index 0000000000..48f7414000
--- /dev/null
+++ b/.changeset/polite-houses-design.md
@@ -0,0 +1,5 @@
+---
+"supi": patch
+---
+
+Don't ignore the "overrides" field when install/update doesn't include the root project.
diff --git a/packages/supi/src/install/index.ts b/packages/supi/src/install/index.ts
index 3e84267a7a..c17fdbbd55 100644
--- a/packages/supi/src/install/index.ts
+++ b/packages/supi/src/install/index.ts
@@ -137,12 +137,15 @@ export async function mutateModules (
   const installsOnly = projects.every((project) => project.mutation === 'install')
   opts['forceNewModules'] = installsOnly
   const ctx = await getContext(projects, opts)
-  const rootProject = ctx.projects.find(({ id }) => id === '.')
+  const rootProjectManifest = ctx.projects.find(({ id }) => id === '.')?.manifest ??
+    // When running install/update on a subset of projects, the root project might not be included,
+    // so reading its manifest explicitly hear.
+    await safeReadProjectManifestOnly(opts.lockfileDir)
   // We read Yarn's resolutions field for compatibility
   // but we really replace the version specs to any other version spec, not only to exact versions,
   // so we cannot call it resolutions
-  const overrides = rootProject
-    ? rootProject.manifest.pnpm?.overrides ?? rootProject.manifest.resolutions
+  const overrides = rootProjectManifest
+    ? rootProjectManifest.pnpm?.overrides ?? rootProjectManifest.resolutions
     : undefined
   if (!R.isEmpty(overrides ?? {})) {
     const versionsOverrider = createVersionsOverrider(overrides!)