diff --git a/src/dnvm/PruneCommand.cs b/src/dnvm/PruneCommand.cs
index 8d0d83d..19c4e10 100644
--- a/src/dnvm/PruneCommand.cs
+++ b/src/dnvm/PruneCommand.cs
@@ -54,7 +54,7 @@ public static async Task<int> Run(DnvmEnv env, Logger logger, Options options)
                 if (!manifest.IsSdkInstalled(sdk.Version, sdk.Dir))
                 {
                     env.Console.Warn($"SDK {sdk.Version} was not found in installed SDKs, cleaning up stale manifest entry.");
-                    manifest = RemoveSdkFromChannels(manifest, sdk.Version);
+                    manifest = RemoveSdkFromChannels(manifest, sdk.Version, sdk.Dir);
                     await @lock.WriteManifest(env, manifest);
                     continue;
                 }
@@ -110,18 +110,26 @@ public static async Task<int> Run(DnvmEnv env, Logger logger, Options options)
             }
         }
 
-        return sdksToRemove;
+        return sdksToRemove.Distinct().ToList();
     }
 
     /// <summary>
-    /// Removes an SDK version from all RegisteredChannels.InstalledSdkVersions.
+    /// Removes an SDK version from RegisteredChannels.InstalledSdkVersions for one SDK directory.
     /// This is used to clean up stale entries left by a bug fixed in
     /// https://github.com/dn-vm/dnvm/pull/274.
     /// </summary>
-    private static Manifest RemoveSdkFromChannels(Manifest manifest, SemVersion sdkVersion)
+    private static Manifest RemoveSdkFromChannels(
+        Manifest manifest,
+        SemVersion sdkVersion,
+        SdkDirName sdkDir)
     {
         var updatedChannels = manifest.RegisteredChannels.Select(channel =>
         {
+            if (channel.SdkDirName != sdkDir)
+            {
+                return channel;
+            }
+
             var updatedInstalledVersions = channel.InstalledSdkVersions
                 .Where(version => version != sdkVersion)
                 .ToEq();
diff --git a/src/dnvm/UninstallCommand.cs b/src/dnvm/UninstallCommand.cs
index fbe1762..61641da 100644
--- a/src/dnvm/UninstallCommand.cs
+++ b/src/dnvm/UninstallCommand.cs
@@ -71,7 +71,7 @@ public static async Task<int> Run(ManifestLock @lock, DnvmEnv env, Logger logger
         DeleteAspnets(env, aspnetToRemove, logger);
         DeleteWins(env, winToRemove, logger);
 
-        manifest = UninstallSdk(manifest, sdkVersion);
+        manifest = UninstallSdks(manifest, sdksToRemove);
         await @lock.WriteManifest(env, manifest);
 
         return 0;
@@ -137,18 +137,18 @@ private static void DeleteWins(DnvmEnv env, IEnumerable<(SemVersion, SdkDirName)
         }
     }
 
-    private static Manifest UninstallSdk(Manifest manifest, SemVersion sdkVersion)
+    private static Manifest UninstallSdks(
+        Manifest manifest,
+        HashSet<(SemVersion Version, SdkDirName Dir)> sdksToRemove)
     {
-        // Delete SDK version from all directories
         var newVersions = manifest.InstalledSdks
-            .Where(sdk => sdk.SdkVersion != sdkVersion)
+            .Where(sdk => !sdksToRemove.Contains((sdk.SdkVersion, sdk.SdkDirName)))
             .ToEq();
 
-        // Also remove the SDK version from RegisteredChannels.InstalledSdkVersions
         var updatedChannels = manifest.RegisteredChannels.Select(channel =>
         {
             var updatedInstalledVersions = channel.InstalledSdkVersions
-                .Where(version => version != sdkVersion)
+                .Where(version => !sdksToRemove.Contains((version, channel.SdkDirName)))
                 .ToEq();
             return channel with { InstalledSdkVersions = updatedInstalledVersions };
         }).ToEq();
diff --git a/test/UnitTests/PruneTests.cs b/test/UnitTests/PruneTests.cs
index c5f131f..dd536cc 100644
--- a/test/UnitTests/PruneTests.cs
+++ b/test/UnitTests/PruneTests.cs
@@ -178,6 +178,58 @@ public Task MissingDirectoriesHandled() => RunWithServer(async (server, env) =>
         Assert.Equal(upgradeVersion, finalManifest.InstalledSdks[0].SdkVersion);
     });
 
+    [Fact]
+    public Task StaleCleanupDoesNotAffectOtherSdkDirectories() => RunWithServer(async (server, env) =>
+    {
+        var oldVersion = new SemVersion(8, 0, 100);
+        var newVersion = new SemVersion(8, 0, 101);
+        var defaultDir = DnvmEnv.DefaultSdkDirName;
+        var alternateDir = new SdkDirName("alternate");
+
+        var manifest = Manifest.Empty
+            .AddSdk(oldVersion, sdkDirParam: defaultDir)
+            .AddSdk(newVersion, sdkDirParam: defaultDir)
+            .AddSdk(oldVersion, sdkDirParam: alternateDir);
+        manifest = manifest with
+        {
+            RegisteredChannels =
+            [
+                new RegisteredChannel
+                {
+                    ChannelName = new Channel.Latest(),
+                    SdkDirName = defaultDir,
+                    InstalledSdkVersions = [oldVersion, newVersion],
+                },
+                new RegisteredChannel
+                {
+                    ChannelName = new Channel.VersionedMajorMinor(8, 0),
+                    SdkDirName = defaultDir,
+                    InstalledSdkVersions = [oldVersion, newVersion],
+                },
+                new RegisteredChannel
+                {
+                    ChannelName = new Channel.VersionedMajorMinor(8, 0),
+                    SdkDirName = alternateDir,
+                    InstalledSdkVersions = [oldVersion],
+                },
+            ]
+        };
+        await Manifest.WriteManifestUnsafe(env, manifest);
+
+        Assert.Equal(
+            [(oldVersion, defaultDir)],
+            PruneCommand.GetOutOfDateSdks(manifest));
+
+        Assert.Equal(0, await PruneCommand.Run(env, _logger, new PruneCommand.Options()));
+
+        var finalManifest = await Manifest.ReadManifestUnsafe(env);
+        Assert.Contains(finalManifest.InstalledSdks,
+            sdk => sdk.SdkVersion == oldVersion && sdk.SdkDirName == alternateDir);
+        Assert.Contains(finalManifest.RegisteredChannels,
+            channel => channel.SdkDirName == alternateDir
+                && channel.InstalledSdkVersions.Contains(oldVersion));
+    });
+
     /// <summary>
     /// Tests the scenario from https://github.com/dn-vm/dnvm/issues/311:
     /// Before PR #274, uninstalling an SDK removed it from InstalledSdks but not from