diff --git a/src/dnvm/PruneCommand.cs b/src/dnvm/PruneCommand.cs
index 08da401..8d0d83d 100644
--- a/src/dnvm/PruneCommand.cs
+++ b/src/dnvm/PruneCommand.cs
@@ -48,12 +48,25 @@ public static async Task<int> Run(DnvmEnv env, Logger logger, Options options)
             }
             else
             {
+                // Check if the SDK is actually in InstalledSdks. It may not be if the manifest
+                // was corrupted by a bug fixed in https://github.com/dn-vm/dnvm/pull/274.
+                // In that case, we just need to clean up the stale entry from RegisteredChannels.
+                if (!manifest.IsSdkInstalled(sdk.Version, sdk.Dir))
+                {
+                    env.Console.Warn($"SDK {sdk.Version} was not found in installed SDKs, cleaning up stale manifest entry.");
+                    manifest = RemoveSdkFromChannels(manifest, sdk.Version);
+                    await @lock.WriteManifest(env, manifest);
+                    continue;
+                }
+
                 Console.WriteLine($"Removing {sdk}");
                 int result = await UninstallCommand.Run(@lock, env, logger, sdk.Version, sdk.Dir);
                 if (result != 0)
                 {
                     return result;
                 }
+                // Re-read manifest after uninstall since it was modified
+                manifest = await @lock.ReadManifest(env);
             }
         }
         return 0;
@@ -99,4 +112,22 @@ public static async Task<int> Run(DnvmEnv env, Logger logger, Options options)
 
         return sdksToRemove;
     }
+
+    /// <summary>
+    /// Removes an SDK version from all RegisteredChannels.InstalledSdkVersions.
+    /// 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)
+    {
+        var updatedChannels = manifest.RegisteredChannels.Select(channel =>
+        {
+            var updatedInstalledVersions = channel.InstalledSdkVersions
+                .Where(version => version != sdkVersion)
+                .ToEq();
+            return channel with { InstalledSdkVersions = updatedInstalledVersions };
+        }).ToEq();
+
+        return manifest with { RegisteredChannels = updatedChannels };
+    }
 }
\ No newline at end of file
diff --git a/test/UnitTests/PruneTests.cs b/test/UnitTests/PruneTests.cs
index 79df449..c5f131f 100644
--- a/test/UnitTests/PruneTests.cs
+++ b/test/UnitTests/PruneTests.cs
@@ -177,4 +177,65 @@ public Task MissingDirectoriesHandled() => RunWithServer(async (server, env) =>
         Assert.Single(finalManifest.InstalledSdks);
         Assert.Equal(upgradeVersion, finalManifest.InstalledSdks[0].SdkVersion);
     });
+
+    /// <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
+    /// RegisteredChannels.InstalledSdkVersions. Prune should handle this gracefully by
+    /// logging a warning and cleaning up the stale manifest entry.
+    /// </summary>
+    [Fact]
+    public Task PruneHandlesCorruptedManifestFromPre274Uninstall() => RunWithServer(async (server, env) =>
+    {
+        var oldVersion = SemVersion.Parse("8.0.100", SemVersionStyles.Strict);
+        var newVersion = SemVersion.Parse("8.0.101", SemVersionStyles.Strict);
+        Channel channel = new Channel.Latest();
+
+        // Create a corrupted manifest that simulates the state left by a pre-PR#274 uninstall:
+        // - The old SDK version is in RegisteredChannels.InstalledSdkVersions (was not removed)
+        // - But the old SDK is NOT in InstalledSdks (was removed)
+        // - The new SDK is properly tracked in both places
+        var corruptedManifest = Manifest.Empty with
+        {
+            InstalledSdks = [
+                // Only the new version is in InstalledSdks (old version was uninstalled)
+                new InstalledSdk
+                {
+                    SdkVersion = newVersion,
+                    RuntimeVersion = newVersion,
+                    AspNetVersion = newVersion,
+                    ReleaseVersion = newVersion,
+                    SdkDirName = DnvmEnv.DefaultSdkDirName
+                }
+            ],
+            RegisteredChannels = [
+                new RegisteredChannel
+                {
+                    ChannelName = channel,
+                    SdkDirName = DnvmEnv.DefaultSdkDirName,
+                    // Bug: old version is still in InstalledSdkVersions even though it was uninstalled
+                    InstalledSdkVersions = [oldVersion, newVersion]
+                }
+            ]
+        };
+
+        await Manifest.WriteManifestUnsafe(env, corruptedManifest);
+
+        var console = (TestConsole)env.Console;
+        var initialOutput = console.Output;
+
+        // Prune should succeed and clean up the stale manifest entry
+        var pruneResult = await PruneCommand.Run(env, _logger, new PruneCommand.Options());
+
+        var output = console.Output[initialOutput.Length..];
+
+        Assert.Equal(0, pruneResult);
+        Assert.Contains("was not found in installed SDKs", output);
+
+        // Verify the manifest was cleaned up - old version should be removed from channel
+        var finalManifest = await Manifest.ReadManifestUnsafe(env);
+        var registeredChannel = Assert.Single(finalManifest.RegisteredChannels);
+        Assert.Single(registeredChannel.InstalledSdkVersions);
+        Assert.Equal(newVersion, registeredChannel.InstalledSdkVersions[0]);
+    });
 }
\ No newline at end of file