diff --git a/crates/goose-server/src/openapi.rs b/crates/goose-server/src/openapi.rs
index 692a704d..ae8bc4d5 100644
--- a/crates/goose-server/src/openapi.rs
+++ b/crates/goose-server/src/openapi.rs
@@ -12,6 +12,7 @@ use utoipa::OpenApi;
 #[derive(OpenApi)]
 #[openapi(
     paths(
+        super::routes::config_management::init_config,
         super::routes::config_management::upsert_config,
         super::routes::config_management::remove_config,
         super::routes::config_management::read_config,
diff --git a/crates/goose-server/src/routes/config_management.rs b/crates/goose-server/src/routes/config_management.rs
index 0313be74..7d529603 100644
--- a/crates/goose-server/src/routes/config_management.rs
+++ b/crates/goose-server/src/routes/config_management.rs
@@ -14,6 +14,7 @@ use goose::providers::providers as get_providers;
 use http::{HeaderMap, StatusCode};
 use serde::{Deserialize, Serialize};
 use serde_json::Value;
+use serde_yaml;
 use std::collections::HashMap;
 use utoipa::ToSchema;
 
@@ -320,6 +321,75 @@ pub async fn providers(
     Ok(Json(providers_response))
 }
 
+#[utoipa::path(
+    post,
+    path = "/config/init",
+    responses(
+        (status = 200, description = "Config initialization check completed", body = String),
+        (status = 500, description = "Internal server error")
+    )
+)]
+pub async fn init_config(
+    State(state): State<AppState>,
+    headers: HeaderMap,
+) -> Result<Json<String>, StatusCode> {
+    verify_secret_key(&headers, &state)?;
+
+    let config = Config::global();
+
+    // 200 if config already exists
+    if config.exists() {
+        return Ok(Json("Config already exists".to_string()));
+    }
+
+    // Find the workspace root (where the top-level Cargo.toml with [workspace] is)
+    let workspace_root = match std::env::current_exe() {
+        Ok(mut exe_path) => {
+            // Start from the executable's directory and traverse up
+            while let Some(parent) = exe_path.parent() {
+                let cargo_toml = parent.join("Cargo.toml");
+                if cargo_toml.exists() {
+                    // Read the Cargo.toml file
+                    if let Ok(content) = std::fs::read_to_string(&cargo_toml) {
+                        // Check if it contains [workspace]
+                        if content.contains("[workspace]") {
+                            exe_path = parent.to_path_buf();
+                            break;
+                        }
+                    }
+                }
+                exe_path = parent.to_path_buf();
+            }
+            exe_path
+        }
+        Err(_) => return Err(StatusCode::INTERNAL_SERVER_ERROR),
+    };
+
+    // Check if init-config.yaml exists at workspace root
+    let init_config_path = workspace_root.join("init-config.yaml");
+    if !init_config_path.exists() {
+        return Ok(Json(
+            "No init-config.yaml found, using default configuration".to_string(),
+        ));
+    }
+
+    // Read init-config.yaml and validate
+    let init_content = match std::fs::read_to_string(&init_config_path) {
+        Ok(content) => content,
+        Err(_) => return Err(StatusCode::INTERNAL_SERVER_ERROR),
+    };
+    let init_values: HashMap<String, Value> = match serde_yaml::from_str(&init_content) {
+        Ok(values) => values,
+        Err(_) => return Err(StatusCode::INTERNAL_SERVER_ERROR),
+    };
+
+    // Save init-config.yaml to ~/.config/goose/config.yaml
+    match config.save_values(init_values) {
+        Ok(_) => Ok(Json("Config initialized successfully".to_string())),
+        Err(_) => Err(StatusCode::INTERNAL_SERVER_ERROR),
+    }
+}
+
 pub fn routes(state: AppState) -> Router {
     Router::new()
         .route("/config", get(read_all_config))
@@ -330,5 +400,6 @@ pub fn routes(state: AppState) -> Router {
         .route("/config/extensions", post(add_extension))
         .route("/config/extensions/:name", delete(remove_extension))
         .route("/config/providers", get(providers))
+        .route("/config/init", post(init_config))
         .with_state(state)
 }
diff --git a/crates/goose/src/config/base.rs b/crates/goose/src/config/base.rs
index 8367c4f5..4f11f3f5 100644
--- a/crates/goose/src/config/base.rs
+++ b/crates/goose/src/config/base.rs
@@ -210,7 +210,7 @@ impl Config {
     }
 
     // Save current values to the config file
-    fn save_values(&self, values: HashMap<String, Value>) -> Result<(), ConfigError> {
+    pub fn save_values(&self, values: HashMap<String, Value>) -> Result<(), ConfigError> {
         // Convert to YAML for storage
         let yaml_value = serde_yaml::to_string(&values)?;
 
diff --git a/ui/desktop/openapi.json b/ui/desktop/openapi.json
index c69d0f92..fb07b085 100644
--- a/ui/desktop/openapi.json
+++ b/ui/desktop/openapi.json
@@ -173,6 +173,29 @@
         }
       }
     },
+    "/config/init": {
+      "post": {
+        "tags": [
+          "super::routes::config_management"
+        ],
+        "operationId": "init_config",
+        "responses": {
+          "200": {
+            "description": "Config initialization check completed",
+            "content": {
+              "text/plain": {
+                "schema": {
+                  "type": "string"
+                }
+              }
+            }
+          },
+          "500": {
+            "description": "Internal server error"
+          }
+        }
+      }
+    },
     "/config/providers": {
       "get": {
         "tags": [
diff --git a/ui/desktop/src/App.tsx b/ui/desktop/src/App.tsx
index 82862c3d..f23a4a79 100644
--- a/ui/desktop/src/App.tsx
+++ b/ui/desktop/src/App.tsx
@@ -31,6 +31,7 @@ import { useChat } from './hooks/useChat';
 import 'react-toastify/dist/ReactToastify.css';
 import { useConfig, MalformedConfigError } from './components/ConfigContext';
 import { addExtensionFromDeepLink as addExtensionFromDeepLinkV2 } from './components/settings_v2/extensions';
+import { initConfig } from './api/sdk.gen';
 
 // Views and their options
 export type View =
@@ -91,6 +92,9 @@ export default function App() {
 
     const initializeApp = async () => {
       try {
+        // Initialize config first
+        await initConfig();
+
         const config = window.electron.getConfig();
 
         const provider = (await read('GOOSE_PROVIDER', false)) ?? config.GOOSE_DEFAULT_PROVIDER;
diff --git a/ui/desktop/src/api/sdk.gen.ts b/ui/desktop/src/api/sdk.gen.ts
index 94058a79..66010de1 100644
--- a/ui/desktop/src/api/sdk.gen.ts
+++ b/ui/desktop/src/api/sdk.gen.ts
@@ -1,7 +1,7 @@
 // This file is auto-generated by @hey-api/openapi-ts
 
 import type { Options as ClientOptions, TDataShape, Client } from '@hey-api/client-fetch';
-import type { GetToolsData, GetToolsResponse, ReadAllConfigData, ReadAllConfigResponse, GetExtensionsData, GetExtensionsResponse, AddExtensionData, AddExtensionResponse, RemoveExtensionData, RemoveExtensionResponse, ProvidersData, ProvidersResponse2, ReadConfigData, RemoveConfigData, RemoveConfigResponse, UpsertConfigData, UpsertConfigResponse } from './types.gen';
+import type { GetToolsData, GetToolsResponse, ReadAllConfigData, ReadAllConfigResponse, GetExtensionsData, GetExtensionsResponse, AddExtensionData, AddExtensionResponse, RemoveExtensionData, RemoveExtensionResponse, InitConfigData, InitConfigResponse, ProvidersData, ProvidersResponse2, ReadConfigData, RemoveConfigData, RemoveConfigResponse, UpsertConfigData, UpsertConfigResponse } from './types.gen';
 import { client as _heyApiClient } from './client.gen';
 
 export type Options<TData extends TDataShape = TDataShape, ThrowOnError extends boolean = boolean> = ClientOptions<TData, ThrowOnError> & {
@@ -57,6 +57,13 @@ export const removeExtension = <ThrowOnError extends boolean = false>(options: O
     });
 };
 
+export const initConfig = <ThrowOnError extends boolean = false>(options?: Options<InitConfigData, ThrowOnError>) => {
+    return (options?.client ?? _heyApiClient).post<InitConfigResponse, unknown, ThrowOnError>({
+        url: '/config/init',
+        ...options
+    });
+};
+
 export const providers = <ThrowOnError extends boolean = false>(options?: Options<ProvidersData, ThrowOnError>) => {
     return (options?.client ?? _heyApiClient).get<ProvidersResponse2, unknown, ThrowOnError>({
         url: '/config/providers',
diff --git a/ui/desktop/src/api/types.gen.ts b/ui/desktop/src/api/types.gen.ts
index 3392d5e7..75e2e016 100644
--- a/ui/desktop/src/api/types.gen.ts
+++ b/ui/desktop/src/api/types.gen.ts
@@ -360,6 +360,29 @@ export type RemoveExtensionResponses = {
 
 export type RemoveExtensionResponse = RemoveExtensionResponses[keyof RemoveExtensionResponses];
 
+export type InitConfigData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: '/config/init';
+};
+
+export type InitConfigErrors = {
+    /**
+     * Internal server error
+     */
+    500: unknown;
+};
+
+export type InitConfigResponses = {
+    /**
+     * Config initialization check completed
+     */
+    200: string;
+};
+
+export type InitConfigResponse = InitConfigResponses[keyof InitConfigResponses];
+
 export type ProvidersData = {
     body?: never;
     path?: never;