diff --git a/crates/goose-api/src/main.rs b/crates/goose-api/src/main.rs
index 0e6e01dd..33efaf65 100644
--- a/crates/goose-api/src/main.rs
+++ b/crates/goose-api/src/main.rs
@@ -2,6 +2,7 @@ use warp::{Filter, Rejection};
 use warp::http::HeaderValue;
 use serde::{Deserialize, Serialize};
 use std::sync::LazyLock;
+use goose::config::{Config, ExtensionEntry};
 use goose::agents::{
     extension::Envs,
     Agent,
@@ -11,7 +12,7 @@ use goose::agents::{
 use mcp_core::tool::Tool;
 use std::collections::HashMap;
 use uuid::Uuid;
-use goose::config::Config;
+
 use goose::providers::{create, providers};
 use goose::model::ModelConfig;
 use goose::message::Message;
@@ -510,17 +511,20 @@ async fn initialize_provider_config() -> Result<(), anyhow::Error> {
     Ok(())
 }
 /// Initialize extensions from the configuration.
-fn initialize_extensions(config: &config::Config) -> Result<(), anyhow::Error> {
+async fn initialize_extensions(config: &config::Config) -> Result<(), anyhow::Error> {
     if let Ok(ext_table) = config.get_table("extensions") {
         for (name, ext_config) in ext_table {
-            let json_value: serde_json::Value = ext_config.clone().try_deserialize()
+            // Deserialize into ExtensionEntry to get enabled flag and config
+            let entry: ExtensionEntry = ext_config.clone().try_deserialize()
                 .map_err(|e| anyhow::anyhow!("Failed to deserialize extension config for {}: {}", name, e))?;
-            // Only process the extension if it is enabled.
-            let enabled = json_value.get("enabled").and_then(|v| v.as_bool()).unwrap_or(false);
-            if enabled {
-                // Note: The ExtensionManager does not provide a method to register extensions.
-                // Here, we log that the extension is enabled. Adjust this code if a registration API becomes available.
-                info!("Extension {} is enabled and would be registered", name);
+
+            if entry.enabled {
+                let extension_config: ExtensionConfig = entry.config;
+                // Acquire the global agent lock and try to add the extension
+                let mut agent = AGENT.lock().await;
+                if let Err(e) = agent.add_extension(extension_config).await {
+                    error!("Failed to add extension {}: {}", name, e);
+                }
             } else {
                 info!("Skipping disabled extension: {}", name);
             }
@@ -569,7 +573,7 @@ async fn main() -> Result<(), anyhow::Error> {
     }
     
     // Initialize extensions from configuration
-    if let Err(e) = initialize_extensions(&api_config) {
+    if let Err(e) = initialize_extensions(&api_config).await {
         error!("Failed to initialize extensions: {}", e);
     }