diff --git a/Keybinding.Test/SaveWithoutInitializeTests.cs b/Keybinding.Test/SaveWithoutInitializeTests.cs
new file mode 100644
index 0000000..939144e
--- /dev/null
+++ b/Keybinding.Test/SaveWithoutInitializeTests.cs
@@ -0,0 +1,90 @@
+// Copyright (c) 2023-2026 ktsu-dev contributors
+
+namespace ktsu.Keybinding.Test;
+
+using ktsu.Keybinding.Core;
+using ktsu.Keybinding.Core.Models;
+
+[TestClass]
+public class SaveWithoutInitializeTests
+{
+	private string _testDataDirectory = null!;
+
+	[TestInitialize]
+	public void Setup()
+	{
+		_testDataDirectory = Path.Combine(Path.GetTempPath(), Guid.NewGuid().ToString());
+		Directory.CreateDirectory(_testDataDirectory);
+	}
+
+	[TestCleanup]
+	public void Cleanup()
+	{
+		if (Directory.Exists(_testDataDirectory))
+		{
+			Directory.Delete(_testDataDirectory, recursive: true);
+		}
+	}
+
+	private async Task<string> LoadProfileIdsAsync()
+	{
+		using KeybindingManager manager = new(_testDataDirectory);
+		await manager.InitializeAsync().ConfigureAwait(false);
+		return string.Join(',', manager.Profiles.GetAllProfiles().Select(p => p.Id).Order(StringComparer.Ordinal));
+	}
+
+	[TestMethod]
+	public async Task SaveAsync_WithoutInitialize_KeepsStoredProfiles()
+	{
+		{
+			using KeybindingManager manager = new(_testDataDirectory);
+			await manager.InitializeAsync().ConfigureAwait(false);
+			manager.CreateDefaultProfile();
+			manager.Profiles.CreateProfile("vim", "Vim");
+			await manager.SaveAsync().ConfigureAwait(false);
+		}
+
+		{
+			using KeybindingManager manager = new(_testDataDirectory);
+			manager.CreateDefaultProfile("other", "Other");
+			await manager.SaveAsync().ConfigureAwait(false);
+		}
+
+		Assert.AreEqual("default,other,vim", await LoadProfileIdsAsync().ConfigureAwait(false));
+	}
+
+	[TestMethod]
+	public async Task DeleteProfile_CreatedAndSavedInSameManager_StaysDeleted()
+	{
+		{
+			using KeybindingManager manager = new(_testDataDirectory);
+			manager.Profiles.CreateProfile("default", "Default");
+			manager.Profiles.CreateProfile("vim", "Vim");
+			await manager.SaveAsync().ConfigureAwait(false);
+
+			Assert.IsTrue(manager.Profiles.DeleteProfile("vim"));
+			await manager.SaveAsync().ConfigureAwait(false);
+		}
+
+		Assert.AreEqual("default", await LoadProfileIdsAsync().ConfigureAwait(false));
+	}
+
+	[TestMethod]
+	public async Task DeleteProfile_ThenRecreate_IsSavedAgain()
+	{
+		{
+			using KeybindingManager manager = new(_testDataDirectory);
+			await manager.InitializeAsync().ConfigureAwait(false);
+			manager.Profiles.CreateProfile("vim", "Vim");
+			await manager.SaveAsync().ConfigureAwait(false);
+
+			Assert.IsTrue(manager.Profiles.DeleteProfile("vim"));
+			await manager.SaveAsync().ConfigureAwait(false);
+
+			manager.Profiles.CreateProfile(new Profile("vim", "Vim again"));
+			await manager.SaveAsync().ConfigureAwait(false);
+		}
+
+		Assert.AreEqual("vim", await LoadProfileIdsAsync().ConfigureAwait(false));
+	}
+}
diff --git a/Keybinding/KeybindingManager.cs b/Keybinding/KeybindingManager.cs
index 1717799..66c4ae3 100644
--- a/Keybinding/KeybindingManager.cs
+++ b/Keybinding/KeybindingManager.cs
@@ -13,6 +13,12 @@ namespace ktsu.Keybinding.Core;
 public sealed class KeybindingManager : IDisposable
 {
 	private bool _disposed;
+
+	// Ids of the stored profiles this manager has loaded or saved. SaveAsync deletes a stored profile only if
+	// it is in here and no longer in memory, so profiles this manager never saw are not taken as deleted.
+	private readonly HashSet<string> _persistedProfileIds = [];
+	private readonly Lock _persistedProfileIdsLock = new();
+
 	/// <summary>
 	/// Initializes a new instance of the <see cref="KeybindingManager"/> class with default services
 	/// </summary>
@@ -87,6 +93,11 @@ public async Task InitializeAsync()
 			Profiles.CreateProfile(profile);
 		}
 
+		lock (_persistedProfileIdsLock)
+		{
+			_persistedProfileIds.UnionWith(profiles.Select(p => p.Id));
+		}
+
 		// Load active profile
 		string? activeProfileId = await Repository.LoadActiveProfileAsync().ConfigureAwait(false);
 		if (!string.IsNullOrEmpty(activeProfileId) && Profiles.ProfileExists(activeProfileId))
@@ -107,16 +118,28 @@ public async Task SaveAsync()
 		IReadOnlyCollection<Command> commands = Commands.GetAllCommands();
 		await Repository.SaveCommandsAsync(commands).ConfigureAwait(false);
 
-		// Remove stored profiles that were deleted in memory, so they do not come back on the next load
+		// Remove stored profiles that were deleted in memory, so they do not come back on the next load. Only
+		// profiles this manager loaded or saved count: one it never saw is not in memory because it was never
+		// loaded, not because it was deleted.
 		IReadOnlyCollection<Profile> profiles = Profiles.GetAllProfiles();
 		HashSet<string> profileIds = [.. profiles.Select(p => p.Id)];
-		IReadOnlyCollection<Profile> storedProfiles = await Repository.LoadAllProfilesAsync().ConfigureAwait(false);
-		IEnumerable<string> deletedProfileIds = storedProfiles.Select(p => p.Id).Where(id => !profileIds.Contains(id));
+		List<string> deletedProfileIds;
+		lock (_persistedProfileIdsLock)
+		{
+			deletedProfileIds = [.. _persistedProfileIds.Where(id => !profileIds.Contains(id))];
+		}
+
 		await AsyncBatchHelper.ForEachAsync(deletedProfileIds, Repository.DeleteProfileAsync).ConfigureAwait(false);
 
 		// Save profiles using batch helper
 		await AsyncBatchHelper.ForEachAsync(profiles, Repository.SaveProfileAsync).ConfigureAwait(false);
 
+		lock (_persistedProfileIdsLock)
+		{
+			_persistedProfileIds.ExceptWith(deletedProfileIds);
+			_persistedProfileIds.UnionWith(profileIds);
+		}
+
 		// Save active profile
 		Profile? activeProfile = Profiles.GetActiveProfile();
 		await Repository.SaveActiveProfileAsync(activeProfile?.Id).ConfigureAwait(false);