diff --git a/crates/turborepo-lockfiles/fixtures/pnpm-injected-file.yaml b/crates/turborepo-lockfiles/fixtures/pnpm-injected-file.yaml
new file mode 100644
index 0000000000000..dd964903676dc
--- /dev/null
+++ b/crates/turborepo-lockfiles/fixtures/pnpm-injected-file.yaml
@@ -0,0 +1,18 @@
+lockfileVersion: '9.0'
+
+settings:
+  autoInstallPeers: true
+  excludeLinksFromLockfile: false
+
+importers:
+  services/application:
+    dependencies:
+      library:
+        specifier: workspace:^
+        version: file:../../../libraries/library
+    dependenciesMeta:
+      library:
+        injected: true
+
+packages: {}
+snapshots: {}
\ No newline at end of file
diff --git a/crates/turborepo-lockfiles/fixtures/pnpm-injected-link.yaml b/crates/turborepo-lockfiles/fixtures/pnpm-injected-link.yaml
new file mode 100644
index 0000000000000..8b5602a5912fb
--- /dev/null
+++ b/crates/turborepo-lockfiles/fixtures/pnpm-injected-link.yaml
@@ -0,0 +1,29 @@
+lockfileVersion: '9.0'
+
+settings:
+  autoInstallPeers: true
+  excludeLinksFromLockfile: false
+
+importers:
+  .:
+    devDependencies:
+      turbo:
+        specifier: 2.0.0-canary.0
+        version: 2.0.0-canary.0
+
+  services/application:
+    dependencies:
+      library:
+        specifier: workspace:^
+        version: link:../../../libraries/library
+    dependenciesMeta:
+      library:
+        injected: true
+
+packages:
+  turbo@2.0.0-canary.0:
+    resolution: {integrity: sha512-test}
+    hasBin: true
+
+snapshots:
+  turbo@2.0.0-canary.0: {}
\ No newline at end of file
diff --git a/crates/turborepo-lockfiles/src/pnpm/data.rs b/crates/turborepo-lockfiles/src/pnpm/data.rs
index 9c0cbf8244836..7d2077a6dde11 100644
--- a/crates/turborepo-lockfiles/src/pnpm/data.rs
+++ b/crates/turborepo-lockfiles/src/pnpm/data.rs
@@ -174,6 +174,7 @@ pub struct PackageResolution {
 struct LockfileSettings {
     auto_install_peers: Option<bool>,
     exclude_links_from_lockfile: Option<bool>,
+    inject_workspace_packages: Option<bool>,
 }
 
 impl PnpmLockfile {
@@ -473,10 +474,14 @@ impl crate::Lockfile for PnpmLockfile {
                     .find_resolution(dependency)
                     .ok_or_else(|| Error::MissingInjectedPackage(dependency.clone()))?;
 
-                let entry = self
-                    .get_packages(version)
-                    .ok_or_else(|| crate::Error::MissingPackage(version.into()))?;
-                pruned_packages.insert(version.to_string(), entry.clone());
+                // Skip adding to packages if this is a local workspace link (link: or file: protocol)
+                // These don't have entries in the packages section as they're just symlinks
+                if !version.starts_with("link:") && !version.starts_with("file:") {
+                    let entry = self
+                        .get_packages(version)
+                        .ok_or_else(|| crate::Error::MissingPackage(version.into()))?;
+                    pruned_packages.insert(version.to_string(), entry.clone());
+                }
             }
         }
 
@@ -649,6 +654,10 @@ mod tests {
     const PNPM6_TURBO: &[u8] = include_bytes!("../../fixtures/pnpm6turbo.yaml").as_slice();
     const PNPM8_TURBO: &[u8] = include_bytes!("../../fixtures/pnpm8turbo.yaml").as_slice();
     const PNPM10_PATCH: &[u8] = include_bytes!("../../fixtures/pnpm-10-patch.lock").as_slice();
+    const PNPM_INJECTED_LINK: &[u8] =
+        include_bytes!("../../fixtures/pnpm-injected-link.yaml").as_slice();
+    const PNPM_INJECTED_FILE: &[u8] =
+        include_bytes!("../../fixtures/pnpm-injected-file.yaml").as_slice();
 
     use super::*;
     use crate::{Lockfile, Package};
@@ -1479,4 +1488,30 @@ c:
             crate::Error::MissingWorkspace("apps/docs".to_string()).to_string()
         );
     }
+
+    #[test]
+    fn test_injected_link_dependency_subgraph() {
+        let lockfile = PnpmLockfile::from_bytes(PNPM_INJECTED_LINK).unwrap();
+
+        // This should not error - injected link: dependencies shouldn't require package entries
+        let result = lockfile.subgraph(&["services/application".to_string()], &[]);
+
+        assert!(
+            result.is_ok(),
+            "Subgraph should succeed for injected link: dependencies"
+        );
+    }
+
+    #[test]
+    fn test_injected_file_dependency_subgraph() {
+        let lockfile = PnpmLockfile::from_bytes(PNPM_INJECTED_FILE).unwrap();
+
+        // This should not error - injected file: dependencies shouldn't require package entries
+        let result = lockfile.subgraph(&["services/application".to_string()], &[]);
+
+        assert!(
+            result.is_ok(),
+            "Subgraph should succeed for injected file: dependencies"
+        );
+    }
 }