diff --git a/src/BuslyCLI.Console/Commands/Transport/DeleteTransportCommand.cs b/src/BuslyCLI.Console/Commands/Transport/DeleteTransportCommand.cs
index 9fb70af..bd3b92d 100644
--- a/src/BuslyCLI.Console/Commands/Transport/DeleteTransportCommand.cs
+++ b/src/BuslyCLI.Console/Commands/Transport/DeleteTransportCommand.cs
@@ -15,12 +15,11 @@ public override async Task<int> ExecuteAsync(CommandContext context, DeleteTrans
         {
             if (nsbConfiguration.CurrentTransport.ToLower() == targetTransport)
             {
-                nsbConfiguration.CurrentTransport = "";
+                await nservicebusConfiguration.UpdateCurrentTransportAsync(settings.Config.Path, "");
                 console.WriteLine("This removed your active transport, use \"nservicebus transport set\" to select a different one.");
             }
-            nsbConfiguration.Transports = nsbConfiguration.Transports.Where(x => x.Name.ToLower() != targetTransport).ToList();
+            await nservicebusConfiguration.RemoveTransportAsync(settings.Config.Path, targetTransport);
             console.WriteLine($"deleted transport named {targetTransport} from {settings.Config.Path}");
-            await nservicebusConfiguration.PersistConfiguration(settings.Config.Path, nsbConfiguration);
         }
         else
         {
diff --git a/src/BuslyCLI.Console/Commands/Transport/SetTransportCommand.cs b/src/BuslyCLI.Console/Commands/Transport/SetTransportCommand.cs
index 469eeab..0aa76c2 100644
--- a/src/BuslyCLI.Console/Commands/Transport/SetTransportCommand.cs
+++ b/src/BuslyCLI.Console/Commands/Transport/SetTransportCommand.cs
@@ -13,9 +13,8 @@ public override async Task<int> ExecuteAsync(CommandContext context, SetTranspor
         var targetTransport = settings.TransportName.ToLower();
         if (nsbConfiguration.Transports.Select(x => x.Name.ToLower()).Contains(targetTransport))
         {
-            nsbConfiguration.CurrentTransport = targetTransport;
+            await nservicebusConfiguration.UpdateCurrentTransportAsync(settings.Config.Path, targetTransport);
             console.WriteLine($"Switched to transport \"{targetTransport}\".");
-            await nservicebusConfiguration.PersistConfiguration(settings.Config.Path, nsbConfiguration);
         }
         else
         {
diff --git a/src/BuslyCLI.Console/Config/INServiceBusConfiguration.cs b/src/BuslyCLI.Console/Config/INServiceBusConfiguration.cs
index 14060bd..e57aeb4 100644
--- a/src/BuslyCLI.Console/Config/INServiceBusConfiguration.cs
+++ b/src/BuslyCLI.Console/Config/INServiceBusConfiguration.cs
@@ -10,6 +10,8 @@ public interface INServiceBusConfiguration
     Task<NServiceBusConfig> GetUnValidatedConfigurationAsync(string path);
 
     Task PersistConfiguration(string path, NServiceBusConfig config);
+    Task UpdateCurrentTransportAsync(string path, string newTransport);
+    Task RemoveTransportAsync(string path, string transportToRemove);
 }
 
 public class NServiceBusConfiguration(IDeserializer yamlDeserializer, ISerializer yamlSerializer, IValidator<NServiceBusConfig> validator) : INServiceBusConfiguration
@@ -45,4 +47,55 @@ public async Task PersistConfiguration(string path, NServiceBusConfig config)
         var yaml = yamlSerializer.Serialize(config);
         await File.WriteAllTextAsync(path, yaml);
     }
+
+    public async Task UpdateCurrentTransportAsync(string path, string newTransport)
+    {
+        // Load the YAML
+        var lines = await File.ReadAllLinesAsync(path);
+
+        for (int i = 0; i < lines.Length; i++)
+        {
+            var line = lines[i].TrimStart();
+
+            if (line.StartsWith("current-transport:"))
+            {
+                int indent = lines[i].Length - line.Length; // preserve original indent
+
+                lines[i] =
+                    new string(' ', indent) +
+                    "current-transport: " + newTransport;
+
+                break;
+            }
+        }
+
+        await File.WriteAllLinesAsync(path, lines);
+    }
+
+    public async Task RemoveTransportAsync(string path, string transportToRemove)
+    {
+        var lines = (await File.ReadAllLinesAsync(path)).ToList();
+
+        for (int i = 0; i < lines.Count; i++)
+        {
+            if (lines[i].TrimStart().StartsWith($"- name: {transportToRemove}"))
+            {
+                int indent = lines[i].TakeWhile(char.IsWhiteSpace).Count();
+                int j = i + 1;
+
+                // Continue deleting child lines until indentation decreases
+                while (j < lines.Count &&
+                       lines[j].TakeWhile(char.IsWhiteSpace).Count() > indent)
+                {
+                    j++;
+                }
+
+                // Remove the array item block
+                lines.RemoveRange(i, j - i);
+                break;
+            }
+        }
+
+        await File.WriteAllLinesAsync(path, lines);
+    }
 }
\ No newline at end of file
diff --git a/src/BuslyCLI.Console/Spectre/AppConfiguration.cs b/src/BuslyCLI.Console/Spectre/AppConfiguration.cs
index 15c1433..30ae8f6 100644
--- a/src/BuslyCLI.Console/Spectre/AppConfiguration.cs
+++ b/src/BuslyCLI.Console/Spectre/AppConfiguration.cs
@@ -5,7 +5,6 @@
 using BuslyCLI.Commands.Transport;
 using Spectre.Console;
 using Spectre.Console.Cli;
-using YamlDotNet.Core;
 
 namespace BuslyCLI.Spectre;