diff --git a/src/features/claude-code-agent-loader/loader.ts b/src/features/claude-code-agent-loader/loader.ts
index 407525687..459979428 100644
--- a/src/features/claude-code-agent-loader/loader.ts
+++ b/src/features/claude-code-agent-loader/loader.ts
@@ -44,7 +44,7 @@ function loadAgentsFromDir(agentsDir: string, scope: AgentScope): LoadedAgent[]
 
        const config: AgentConfig = {
          description: formattedDescription,
-         mode: "subagent",
+         mode: data.mode || "subagent",
          prompt: body.trim(),
        }
 
diff --git a/src/features/claude-code-agent-loader/types.ts b/src/features/claude-code-agent-loader/types.ts
index 4ffd9de40..0e6542d25 100644
--- a/src/features/claude-code-agent-loader/types.ts
+++ b/src/features/claude-code-agent-loader/types.ts
@@ -7,6 +7,7 @@ export interface AgentFrontmatter {
   description?: string
   model?: string
   tools?: string
+  mode?: "subagent" | "primary" | "all"
 }
 
 export interface LoadedAgent {
diff --git a/src/plugin-handlers/agent-config-handler.ts b/src/plugin-handlers/agent-config-handler.ts
index 08230f55a..9ceb92460 100644
--- a/src/plugin-handlers/agent-config-handler.ts
+++ b/src/plugin-handlers/agent-config-handler.ts
@@ -198,23 +198,47 @@ export async function applyAgentConfig(params: {
         )
       : undefined;
 
+    // Collect all builtin agent names to prevent user/project .md files from overriding them
+    const builtinAgentNames = new Set([
+      ...Object.keys(agentConfig),
+      ...Object.keys(builtinAgents),
+    ]);
+
+    // Filter user/project agents that duplicate builtin agents (they have mode: "subagent" hardcoded
+    // in loadAgentsFromDir which would incorrectly override the builtin mode: "primary")
+    const filteredUserAgents = Object.fromEntries(
+      Object.entries(userAgents).filter(([key]) => !builtinAgentNames.has(key)),
+    );
+    const filteredProjectAgents = Object.fromEntries(
+      Object.entries(projectAgents).filter(([key]) => !builtinAgentNames.has(key)),
+    );
+
     params.config.agent = {
       ...agentConfig,
       ...Object.fromEntries(
         Object.entries(builtinAgents).filter(([key]) => key !== "sisyphus"),
       ),
-      ...filterDisabledAgents(userAgents),
-      ...filterDisabledAgents(projectAgents),
+      ...filterDisabledAgents(filteredUserAgents),
+      ...filterDisabledAgents(filteredProjectAgents),
       ...filterDisabledAgents(pluginAgents),
       ...filteredConfigAgents,
       build: { ...migratedBuild, mode: "subagent", hidden: true },
       ...(planDemoteConfig ? { plan: planDemoteConfig } : {}),
     };
   } else {
+    // Filter user/project agents that duplicate builtin agents
+    const builtinAgentNames = new Set(Object.keys(builtinAgents));
+    const filteredUserAgents = Object.fromEntries(
+      Object.entries(userAgents).filter(([key]) => !builtinAgentNames.has(key)),
+    );
+    const filteredProjectAgents = Object.fromEntries(
+      Object.entries(projectAgents).filter(([key]) => !builtinAgentNames.has(key)),
+    );
+
     params.config.agent = {
       ...builtinAgents,
-      ...filterDisabledAgents(userAgents),
-      ...filterDisabledAgents(projectAgents),
+      ...filterDisabledAgents(filteredUserAgents),
+      ...filterDisabledAgents(filteredProjectAgents),
       ...filterDisabledAgents(pluginAgents),
       ...configAgent,
     };