diff --git a/dotnet/src/Microsoft.Agents.AI.Hosting.AzureFunctions/DefaultFunctionsAgentOptionsProvider.cs b/dotnet/src/Microsoft.Agents.AI.Hosting.AzureFunctions/DefaultFunctionsAgentOptionsProvider.cs
index 1039fb5aec..4debb5facf 100644
--- a/dotnet/src/Microsoft.Agents.AI.Hosting.AzureFunctions/DefaultFunctionsAgentOptionsProvider.cs
+++ b/dotnet/src/Microsoft.Agents.AI.Hosting.AzureFunctions/DefaultFunctionsAgentOptionsProvider.cs
@@ -6,7 +6,8 @@ namespace Microsoft.Agents.AI.Hosting.AzureFunctions;
 
 /// <summary>
 /// Provides access to agent-specific options for functions agents by name.
-/// Returns default options (HTTP trigger enabled, MCP tool disabled) when no explicit options were configured.
+/// Returns <see langword="false"/> when no explicit options have been configured for an agent,
+/// which distinguishes standalone agents from those auto-registered by workflows.
 /// </summary>
 internal sealed class DefaultFunctionsAgentOptionsProvider(IReadOnlyDictionary<string, FunctionsAgentOptions> functionsAgentOptions)
     : IFunctionsAgentOptionsProvider
@@ -14,32 +15,19 @@ internal sealed class DefaultFunctionsAgentOptionsProvider(IReadOnlyDictionary<s
     private readonly IReadOnlyDictionary<string, FunctionsAgentOptions> _functionsAgentOptions =
         functionsAgentOptions ?? throw new ArgumentNullException(nameof(functionsAgentOptions));
 
-    // Default options. HTTP trigger enabled, MCP tool disabled.
-    private static readonly FunctionsAgentOptions s_defaultOptions = new()
-    {
-        HttpTrigger = { IsEnabled = true },
-        McpToolTrigger = { IsEnabled = false }
-    };
-
     /// <summary>
     /// Attempts to retrieve the options associated with the specified agent name.
-    /// If not found, a default options instance (with HTTP trigger enabled) is returned.
+    /// Returns <see langword="false"/> when no options have been explicitly configured for the agent.
     /// </summary>
     /// <param name="agentName">The name of the agent whose options are to be retrieved. Cannot be null or empty.</param>
-    /// <param name="options">The options for the specified agent. Will never be null.</param>
-    /// <returns>Always true. Returns configured options if present; otherwise default fallback options.</returns>
+    /// <param name="options">
+    /// When this method returns <see langword="true"/>, contains the options for the specified agent;
+    /// otherwise, <see langword="null"/>.
+    /// </param>
+    /// <returns><see langword="true"/> if options were found for the agent; otherwise, <see langword="false"/>.</returns>
     public bool TryGet(string agentName, [NotNullWhen(true)] out FunctionsAgentOptions? options)
     {
         ArgumentException.ThrowIfNullOrEmpty(agentName);
-
-        if (this._functionsAgentOptions.TryGetValue(agentName, out FunctionsAgentOptions? existing))
-        {
-            options = existing;
-            return true;
-        }
-
-        // If not defined, return default options.
-        options = s_defaultOptions;
-        return true;
+        return this._functionsAgentOptions.TryGetValue(agentName, out options);
     }
 }
diff --git a/dotnet/src/Microsoft.Agents.AI.Hosting.AzureFunctions/DurableAgentFunctionMetadataTransformer.cs b/dotnet/src/Microsoft.Agents.AI.Hosting.AzureFunctions/DurableAgentFunctionMetadataTransformer.cs
index 65578a7383..fe20eeb6f9 100644
--- a/dotnet/src/Microsoft.Agents.AI.Hosting.AzureFunctions/DurableAgentFunctionMetadataTransformer.cs
+++ b/dotnet/src/Microsoft.Agents.AI.Hosting.AzureFunctions/DurableAgentFunctionMetadataTransformer.cs
@@ -6,9 +6,13 @@ using Microsoft.Extensions.Logging;
 namespace Microsoft.Agents.AI.Hosting.AzureFunctions;
 
 /// <summary>
-/// Transforms function metadata by registering durable agent functions for each configured agent.
+/// Transforms function metadata by registering durable agent functions for each explicitly configured agent.
 /// </summary>
-/// <remarks>This transformer adds both entity trigger and HTTP trigger functions for every agent registered in the application.</remarks>
+/// <remarks>
+/// This transformer adds entity, HTTP, and MCP tool trigger functions for agents that have
+/// explicit <see cref="FunctionsAgentOptions"/>. Agents auto-registered by workflows
+/// (which lack explicit options) are handled by <see cref="DurableWorkflowsFunctionMetadataTransformer"/>.
+/// </remarks>
 internal sealed class DurableAgentFunctionMetadataTransformer : IFunctionMetadataTransformer
 {
     private readonly ILogger<DurableAgentFunctionMetadataTransformer> _logger;
@@ -38,24 +42,27 @@ internal sealed class DurableAgentFunctionMetadataTransformer : IFunctionMetadat
         {
             string agentName = kvp.Key;
 
-            this._logger.LogRegisteringTriggerForAgent(agentName, "entity");
+            // Only generate triggers for agents with explicit Functions agent options.
+            // Agents auto-registered by workflows are handled by DurableWorkflowsFunctionMetadataTransformer.
+            if (!this._functionsAgentOptionsProvider.TryGet(agentName, out FunctionsAgentOptions? agentTriggerOptions))
+            {
+                continue;
+            }
 
+            this._logger.LogRegisteringTriggerForAgent(agentName, "entity");
             original.Add(FunctionMetadataFactory.CreateEntityTrigger(agentName));
 
-            if (this._functionsAgentOptionsProvider.TryGet(agentName, out FunctionsAgentOptions? agentTriggerOptions))
+            if (agentTriggerOptions.HttpTrigger.IsEnabled)
             {
-                if (agentTriggerOptions.HttpTrigger.IsEnabled)
-                {
-                    this._logger.LogRegisteringTriggerForAgent(agentName, "http");
-                    original.Add(FunctionMetadataFactory.CreateHttpTrigger(agentName, $"agents/{agentName}/run", BuiltInFunctions.RunAgentHttpFunctionEntryPoint));
-                }
+                this._logger.LogRegisteringTriggerForAgent(agentName, "http");
+                original.Add(FunctionMetadataFactory.CreateHttpTrigger(agentName, $"agents/{agentName}/run", BuiltInFunctions.RunAgentHttpFunctionEntryPoint));
+            }
 
-                if (agentTriggerOptions.McpToolTrigger.IsEnabled)
-                {
-                    AIAgent agent = kvp.Value(this._serviceProvider);
-                    this._logger.LogRegisteringTriggerForAgent(agentName, "mcpTool");
-                    original.Add(CreateMcpToolTrigger(agentName, agent.Description));
-                }
+            if (agentTriggerOptions.McpToolTrigger.IsEnabled)
+            {
+                AIAgent agent = kvp.Value(this._serviceProvider);
+                this._logger.LogRegisteringTriggerForAgent(agentName, "mcpTool");
+                original.Add(CreateMcpToolTrigger(agentName, agent.Description));
             }
         }
     }
diff --git a/dotnet/src/Microsoft.Agents.AI.Hosting.AzureFunctions/DurableAgentsOptionsExtensions.cs b/dotnet/src/Microsoft.Agents.AI.Hosting.AzureFunctions/DurableAgentsOptionsExtensions.cs
index ad21d8f4e1..8d161710ae 100644
--- a/dotnet/src/Microsoft.Agents.AI.Hosting.AzureFunctions/DurableAgentsOptionsExtensions.cs
+++ b/dotnet/src/Microsoft.Agents.AI.Hosting.AzureFunctions/DurableAgentsOptionsExtensions.cs
@@ -134,4 +134,17 @@ public static class DurableAgentsOptionsExtensions
     {
         return new Dictionary<string, FunctionsAgentOptions>(s_agentOptions, StringComparer.OrdinalIgnoreCase);
     }
+
+    /// <summary>
+    /// Ensures every agent in <paramref name="agentNames"/> has an entry in the
+    /// options registry. Agents that already have explicit options are left untouched.
+    /// New entries receive the default configuration (HTTP trigger enabled, MCP tool disabled).
+    /// </summary>
+    internal static void EnsureDefaultOptionsForAll(IEnumerable<string> agentNames)
+    {
+        foreach (string name in agentNames)
+        {
+            s_agentOptions.TryAdd(name, new FunctionsAgentOptions { HttpTrigger = { IsEnabled = true } });
+        }
+    }
 }
diff --git a/dotnet/src/Microsoft.Agents.AI.Hosting.AzureFunctions/FunctionsApplicationBuilderExtensions.cs b/dotnet/src/Microsoft.Agents.AI.Hosting.AzureFunctions/FunctionsApplicationBuilderExtensions.cs
index 959ffab2f6..3c5e7936da 100644
--- a/dotnet/src/Microsoft.Agents.AI.Hosting.AzureFunctions/FunctionsApplicationBuilderExtensions.cs
+++ b/dotnet/src/Microsoft.Agents.AI.Hosting.AzureFunctions/FunctionsApplicationBuilderExtensions.cs
@@ -27,9 +27,16 @@ public static class FunctionsApplicationBuilderExtensions
     {
         ArgumentNullException.ThrowIfNull(configure);
 
+        // Create/get shared options BEFORE the DurableTask library call so it can find them.
+        FunctionsDurableOptions sharedOptions = GetOrCreateSharedOptions(builder.Services);
+
         // The main agent services registration is done in Microsoft.DurableTask.Agents.
         builder.Services.ConfigureDurableAgents(configure);
 
+        // Ensure all agents registered through this path have default FunctionsAgentOptions.
+        // This distinguishes them from agents auto-registered by workflows.
+        DurableAgentsOptionsExtensions.EnsureDefaultOptionsForAll(sharedOptions.Agents.GetAgentFactories().Keys);
+
         builder.Services.TryAddSingleton<IFunctionsAgentOptionsProvider>(_ =>
             new DefaultFunctionsAgentOptionsProvider(DurableAgentsOptionsExtensions.GetAgentOptionsSnapshot()));
 
@@ -67,7 +74,7 @@ public static class FunctionsApplicationBuilderExtensions
 
         builder.Services.ConfigureDurableOptions(configure);
 
-        if (sharedOptions.Agents.GetAgentFactories().Count > 0)
+        if (DurableAgentsOptionsExtensions.GetAgentOptionsSnapshot().Count > 0)
         {
             builder.Services.TryAddSingleton<IFunctionsAgentOptionsProvider>(_ =>
                 new DefaultFunctionsAgentOptionsProvider(DurableAgentsOptionsExtensions.GetAgentOptionsSnapshot()));
diff --git a/dotnet/src/Microsoft.Agents.AI.Hosting.AzureFunctions/Workflows/DurableWorkflowsFunctionMetadataTransformer.cs b/dotnet/src/Microsoft.Agents.AI.Hosting.AzureFunctions/Workflows/DurableWorkflowsFunctionMetadataTransformer.cs
index 8066eefccc..dc7b799b00 100644
--- a/dotnet/src/Microsoft.Agents.AI.Hosting.AzureFunctions/Workflows/DurableWorkflowsFunctionMetadataTransformer.cs
+++ b/dotnet/src/Microsoft.Agents.AI.Hosting.AzureFunctions/Workflows/DurableWorkflowsFunctionMetadataTransformer.cs
@@ -50,8 +50,11 @@ internal sealed class DurableWorkflowsFunctionMetadataTransformer : IFunctionMet
         int initialCount = original.Count;
         this._logger.LogTransformingFunctionMetadata(initialCount);
 
-        // Track registered function names to avoid duplicates when workflows share executors.
-        HashSet<string> registeredFunctions = [];
+        // Seed with existing function names to avoid duplicates across transformers
+        // (e.g., when DurableAgentFunctionMetadataTransformer already registered entity triggers).
+        HashSet<string> registeredFunctions = new(
+            original.Select(f => f.Name!),
+            StringComparer.OrdinalIgnoreCase);
 
         DurableWorkflowOptions workflowOptions = this._options.Workflows;
         foreach (var workflow in workflowOptions.Workflows)
diff --git a/dotnet/tests/Microsoft.Agents.AI.Hosting.AzureFunctions.UnitTests/DurableAgentFunctionMetadataTransformerTests.cs b/dotnet/tests/Microsoft.Agents.AI.Hosting.AzureFunctions.UnitTests/DurableAgentFunctionMetadataTransformerTests.cs
index 7d3a2ec13e..82824e0d8c 100644
--- a/dotnet/tests/Microsoft.Agents.AI.Hosting.AzureFunctions.UnitTests/DurableAgentFunctionMetadataTransformerTests.cs
+++ b/dotnet/tests/Microsoft.Agents.AI.Hosting.AzureFunctions.UnitTests/DurableAgentFunctionMetadataTransformerTests.cs
@@ -148,6 +148,45 @@ public sealed class DurableAgentFunctionMetadataTransformerTests
         }
     }
 
+    [Fact]
+    public void Transform_SkipsAgents_WithoutExplicitOptions()
+    {
+        // Arrange: two agents in the dictionary, but only one has explicit FunctionsAgentOptions.
+        // This simulates a workflow-auto-registered agent (workflowAgent) alongside a standalone agent.
+        Dictionary<string, Func<IServiceProvider, AIAgent>> agents = new()
+        {
+            { "standaloneAgent", _ => new TestAgent("standaloneAgent", "Standalone agent") },
+            { "workflowAgent", _ => new TestAgent("workflowAgent", "Auto-registered by workflow") }
+        };
+
+        FunctionsAgentOptions standaloneOptions = new();
+        standaloneOptions.HttpTrigger.IsEnabled = true;
+
+        // Only standaloneAgent has explicit options; workflowAgent does not.
+        IFunctionsAgentOptionsProvider agentOptionsProvider = new FakeOptionsProvider(new Dictionary<string, FunctionsAgentOptions>
+        {
+            { "standaloneAgent", standaloneOptions }
+        });
+
+        List<IFunctionMetadata> metadataList = [];
+
+        DurableAgentFunctionMetadataTransformer transformer = new(
+            agents,
+            NullLogger<DurableAgentFunctionMetadataTransformer>.Instance,
+            new FakeServiceProvider(),
+            agentOptionsProvider);
+
+        // Act
+        transformer.Transform(metadataList);
+
+        // Assert: only standaloneAgent should have triggers (entity + http = 2).
+        // workflowAgent should be skipped entirely.
+        Assert.Equal(2, metadataList.Count);
+        Assert.Contains(metadataList, m => m.Name == "dafx-standaloneAgent");
+        Assert.Contains(metadataList, m => m.Name == "http-standaloneAgent");
+        Assert.DoesNotContain(metadataList, m => m.Name!.Contains("workflowAgent"));
+    }
+
     private static List<IFunctionMetadata> BuildFunctionMetadataList(int numberOfFunctions)
     {
         List<IFunctionMetadata> list = [];