diff --git a/sidecar/src/Kopaya.AgentHost/Services/CopilotWorkflowRunner.cs b/sidecar/src/Kopaya.AgentHost/Services/CopilotWorkflowRunner.cs
index c67b40f..88a625b 100644
--- a/sidecar/src/Kopaya.AgentHost/Services/CopilotWorkflowRunner.cs
+++ b/sidecar/src/Kopaya.AgentHost/Services/CopilotWorkflowRunner.cs
@@ -146,7 +146,7 @@ public sealed class CopilotWorkflowRunner : ITurnWorkflowRunner
             else if (evt is WorkflowOutputEvent outputEvent)
             {
                 List<ChatMessage> allMessages = outputEvent.As<List<ChatMessage>>() ?? [];
-                List<ChatMessage> newMessages = allMessages.Skip(inputMessages.Count).ToList();
+                List<ChatMessage> newMessages = SelectNewOutputMessages(allMessages, inputMessages);
                 completedMessages = ProjectCompletedMessages(
                     command,
                     newMessages,
@@ -369,6 +369,70 @@ public sealed class CopilotWorkflowRunner : ITurnWorkflowRunner
         return mapped;
     }
 
+    internal static List<ChatMessage> SelectNewOutputMessages(
+        IReadOnlyList<ChatMessage> outputMessages,
+        IReadOnlyList<ChatMessage> inputMessages)
+    {
+        if (outputMessages.Count == 0)
+        {
+            return [];
+        }
+
+        if (inputMessages.Count == 0)
+        {
+            return outputMessages.ToList();
+        }
+
+        int overlapLength = FindOutputInputOverlapLength(outputMessages, inputMessages);
+        return outputMessages.Skip(overlapLength).ToList();
+    }
+
+    private static int FindOutputInputOverlapLength(
+        IReadOnlyList<ChatMessage> outputMessages,
+        IReadOnlyList<ChatMessage> inputMessages)
+    {
+        int maxOverlap = Math.Min(outputMessages.Count, inputMessages.Count);
+
+        for (int overlapLength = maxOverlap; overlapLength > 0; overlapLength--)
+        {
+            int inputStart = inputMessages.Count - overlapLength;
+            bool matches = true;
+
+            for (int index = 0; index < overlapLength; index++)
+            {
+                if (!ChatMessagesMatch(inputMessages[inputStart + index], outputMessages[index]))
+                {
+                    matches = false;
+                    break;
+                }
+            }
+
+            if (matches)
+            {
+                return overlapLength;
+            }
+        }
+
+        return 0;
+    }
+
+    private static bool ChatMessagesMatch(ChatMessage inputMessage, ChatMessage outputMessage)
+    {
+        if (inputMessage.Role != outputMessage.Role)
+        {
+            return false;
+        }
+
+        if (!string.Equals(inputMessage.Text, outputMessage.Text, StringComparison.Ordinal))
+        {
+            return false;
+        }
+
+        return string.IsNullOrWhiteSpace(inputMessage.AuthorName)
+            || string.IsNullOrWhiteSpace(outputMessage.AuthorName)
+            || string.Equals(inputMessage.AuthorName, outputMessage.AuthorName, StringComparison.Ordinal);
+    }
+
     private static string ResolveProjectedAuthorName(
         PatternDefinitionDto pattern,
         string? primaryIdentifier,
diff --git a/sidecar/tests/Kopaya.AgentHost.Tests/CopilotWorkflowRunnerTests.cs b/sidecar/tests/Kopaya.AgentHost.Tests/CopilotWorkflowRunnerTests.cs
index e3701af..bedf1b8 100644
--- a/sidecar/tests/Kopaya.AgentHost.Tests/CopilotWorkflowRunnerTests.cs
+++ b/sidecar/tests/Kopaya.AgentHost.Tests/CopilotWorkflowRunnerTests.cs
@@ -6,6 +6,72 @@ namespace Kopaya.AgentHost.Tests;
 
 public sealed class CopilotWorkflowRunnerTests
 {
+    [Fact]
+    public void SelectNewOutputMessages_SkipsFullTranscriptPrefix()
+    {
+        List<ChatMessage> inputMessages =
+        [
+            new(ChatRole.User, "Hello"),
+        ];
+        List<ChatMessage> outputMessages =
+        [
+            new(ChatRole.User, "Hello"),
+            new(ChatRole.Assistant, "Hi there."),
+        ];
+
+        IReadOnlyList<ChatMessage> newMessages = CopilotWorkflowRunner.SelectNewOutputMessages(
+            outputMessages,
+            inputMessages);
+
+        ChatMessage message = Assert.Single(newMessages);
+        Assert.Equal(ChatRole.Assistant, message.Role);
+        Assert.Equal("Hi there.", message.Text);
+    }
+
+    [Fact]
+    public void SelectNewOutputMessages_SkipsOnlyTheLatestInputOverlap()
+    {
+        List<ChatMessage> inputMessages =
+        [
+            new(ChatRole.Assistant, "Earlier answer"),
+            new(ChatRole.User, "Hello"),
+        ];
+        List<ChatMessage> outputMessages =
+        [
+            new(ChatRole.User, "Hello"),
+            new(ChatRole.Assistant, "Hi there."),
+        ];
+
+        IReadOnlyList<ChatMessage> newMessages = CopilotWorkflowRunner.SelectNewOutputMessages(
+            outputMessages,
+            inputMessages);
+
+        ChatMessage message = Assert.Single(newMessages);
+        Assert.Equal(ChatRole.Assistant, message.Role);
+        Assert.Equal("Hi there.", message.Text);
+    }
+
+    [Fact]
+    public void SelectNewOutputMessages_PreservesAssistantOnlyOutput()
+    {
+        List<ChatMessage> inputMessages =
+        [
+            new(ChatRole.User, "Hello"),
+        ];
+        List<ChatMessage> outputMessages =
+        [
+            new(ChatRole.Assistant, "Hi there."),
+        ];
+
+        IReadOnlyList<ChatMessage> newMessages = CopilotWorkflowRunner.SelectNewOutputMessages(
+            outputMessages,
+            inputMessages);
+
+        ChatMessage message = Assert.Single(newMessages);
+        Assert.Equal(ChatRole.Assistant, message.Role);
+        Assert.Equal("Hi there.", message.Text);
+    }
+
     [Fact]
     public void ProjectCompletedMessages_FallsBackToStreamingSegmentsWhenWorkflowOutputIsMissing()
     {