diff --git a/crates/goose/src/agents/extension_manager.rs b/crates/goose/src/agents/extension_manager.rs
index 4736c92a31..e169506cce 100644
--- a/crates/goose/src/agents/extension_manager.rs
+++ b/crates/goose/src/agents/extension_manager.rs
@@ -26,6 +26,7 @@ use tokio_stream::wrappers::ReceiverStream;
 use tokio_util::sync::CancellationToken;
 use tracing::{error, warn};
 
+use super::code_execution_extension::EXTENSION_NAME as CODE_EXECUTION_NAME;
 use super::extension::{
     ExtensionConfig, ExtensionError, ExtensionInfo, ExtensionResult, PlatformExtensionContext,
     ToolInfo, PLATFORM_EXTENSIONS,
@@ -598,12 +599,25 @@ impl ExtensionManager {
             .insert(name, Extension::new(config, client, info, temp_dir));
     }
 
-    /// Get extensions info
+    /// Get extensions info for building the system prompt.
+    /// When code_execution is enabled, it routes tools from other extensions through its
+    /// execute_code interface, so those extensions should not appear as separate sections
+    /// in the system prompt (their instructions would be irrelevant/confusing).
     pub async fn get_extensions_info(&self) -> Vec<ExtensionInfo> {
-        self.extensions
-            .lock()
-            .await
+        let extensions = self.extensions.lock().await;
+        let code_exec_enabled = extensions.contains_key(CODE_EXECUTION_NAME);
+
+        extensions
             .iter()
+            .filter(|(name, _)| {
+                if code_exec_enabled {
+                    // When code_execution is enabled, only show code_execution itself
+                    // Other extensions' tools are accessed via code_execution's execute_code
+                    name.as_str() == CODE_EXECUTION_NAME
+                } else {
+                    true
+                }
+            })
             .map(|(name, ext)| {
                 ExtensionInfo::new(
                     name,
diff --git a/crates/goose/src/agents/prompt_manager.rs b/crates/goose/src/agents/prompt_manager.rs
index af31418acd..b1a17e9d67 100644
--- a/crates/goose/src/agents/prompt_manager.rs
+++ b/crates/goose/src/agents/prompt_manager.rs
@@ -44,6 +44,7 @@ struct SystemPromptContext {
     enable_subagents: bool,
     max_extensions: usize,
     max_tools: usize,
+    code_execution_mode: bool,
 }
 
 pub struct SystemPromptBuilder<'a, M> {
@@ -138,6 +139,11 @@ impl<'a> SystemPromptBuilder<'a, PromptManager> {
             })
             .collect();
 
+        // Detect code_execution mode: when enabled, only code_execution extension is passed
+        let code_execution_mode = sanitized_extensions_info
+            .iter()
+            .any(|ext| ext.name == "code_execution");
+
         let config = Config::global();
         let goose_mode = config.get_goose_mode().unwrap_or(GooseMode::Auto);
 
@@ -155,6 +161,7 @@ impl<'a> SystemPromptBuilder<'a, PromptManager> {
             enable_subagents: should_enabled_subagents(self.model_name.as_str()),
             max_extensions: MAX_EXTENSIONS,
             max_tools: MAX_TOOLS,
+            code_execution_mode,
         };
 
         let base_prompt = if let Some(override_prompt) = &self.manager.system_prompt_override {
diff --git a/crates/goose/src/prompts/system.md b/crates/goose/src/prompts/system.md
index 795934e235..e9743240da 100644
--- a/crates/goose/src/prompts/system.md
+++ b/crates/goose/src/prompts/system.md
@@ -5,6 +5,7 @@ goose uses LLM providers with tool calling capability. You can be used with diff
 claude-sonnet-4, o1, llama-3.2, deepseek-r1, etc).
 These models have varying knowledge cut-off dates depending on when they were trained, but typically it's between 5-10
 months prior to the current date.
+{% if not code_execution_mode %}
 
 # Extensions
 
@@ -40,6 +41,7 @@ and platform__list_resources on this extension.
 {% else %}
 No extensions are defined. You should let the user know that they should add extensions.
 {% endif %}
+{% endif %}
 
 {% if extension_tool_limits is defined %}
 {% with (extension_count, tool_count) = extension_tool_limits  %}