diff --git a/.changes/support-custom-repo-structure.md b/.changes/support-custom-repo-structure.md
new file mode 100644
index 000000000..33ae9c3d2
--- /dev/null
+++ b/.changes/support-custom-repo-structure.md
@@ -0,0 +1,7 @@
+---
+"@tauri-apps/cli": patch:enhance
+"tauri-cli": patch:enhance
+---
+
+Support custom project directory structure where the Tauri app folder is not a subfolder of the frontend project.
+The frontend and Tauri app project paths can be set with the `TAURI_FRONTEND_PATH` and the `TAURI_APP_PATH` environment variables respectively.
diff --git a/crates/tauri-cli/src/helpers/app_paths.rs b/crates/tauri-cli/src/helpers/app_paths.rs
index 74db04236..8ece080ca 100644
--- a/crates/tauri-cli/src/helpers/app_paths.rs
+++ b/crates/tauri-cli/src/helpers/app_paths.rs
@@ -18,6 +18,11 @@ use tauri_utils::{
 };
 
 const TAURI_GITIGNORE: &[u8] = include_bytes!("../../tauri.gitignore");
+// path to the Tauri app (Rust crate) directory, usually <cwd>/src-tauri
+const ENV_TAURI_APP_PATH: &str = "TAURI_APP_PATH";
+// path to the frontend app directory
+const ENV_TAURI_FRONTEND_PATH: &str = "TAURI_FRONTEND_PATH";
+
 static APP_DIR: OnceLock<PathBuf> = OnceLock::new();
 static TAURI_DIR: OnceLock<PathBuf> = OnceLock::new();
 
@@ -68,29 +73,33 @@ fn lookup<F: Fn(&PathBuf) -> bool>(dir: &Path, checker: F) -> Option<PathBuf> {
   None
 }
 
+fn env_tauri_app_path() -> Option<PathBuf> {
+  std::env::var(ENV_TAURI_APP_PATH)
+    .map(PathBuf::from)
+    .ok()?
+    .canonicalize()
+    .ok()
+}
+
+fn env_tauri_frontend_path() -> Option<PathBuf> {
+  std::env::var(ENV_TAURI_FRONTEND_PATH)
+    .map(PathBuf::from)
+    .ok()?
+    .canonicalize()
+    .ok()
+}
+
 pub fn resolve_tauri_dir() -> Option<PathBuf> {
-  let Ok(cwd) = current_dir() else {
-    return None;
-  };
+  let src_dir = env_tauri_frontend_path().or_else(|| current_dir().ok())?;
 
-  if cwd.join(ConfigFormat::Json.into_file_name()).exists()
-    || cwd.join(ConfigFormat::Json5.into_file_name()).exists()
-    || cwd.join(ConfigFormat::Toml.into_file_name()).exists()
+  if src_dir.join(ConfigFormat::Json.into_file_name()).exists()
+    || src_dir.join(ConfigFormat::Json5.into_file_name()).exists()
+    || src_dir.join(ConfigFormat::Toml.into_file_name()).exists()
   {
-    return Some(cwd);
+    return Some(src_dir);
   }
 
-  let src_tauri = cwd.join("src-tauri");
-  if src_tauri.join(ConfigFormat::Json.into_file_name()).exists()
-    || src_tauri
-      .join(ConfigFormat::Json5.into_file_name())
-      .exists()
-    || src_tauri.join(ConfigFormat::Toml.into_file_name()).exists()
-  {
-    return Some(src_tauri);
-  }
-
-  lookup(&cwd, |path| {
+  lookup(&src_dir, |path| {
     folder_has_configuration_file(Target::Linux, path) || is_configuration_file(Target::Linux, path)
   })
   .map(|p| {
@@ -103,13 +112,15 @@ pub fn resolve_tauri_dir() -> Option<PathBuf> {
 }
 
 pub fn resolve() {
-  TAURI_DIR.set(resolve_tauri_dir().unwrap_or_else(||
-    panic!("Couldn't recognize the current folder as a Tauri project. It must contain a `{}`, `{}` or `{}` file in any subfolder.",
+  TAURI_DIR.set(resolve_tauri_dir().unwrap_or_else(|| {
+    let env_var_name = env_tauri_frontend_path().is_some().then(|| format!("`{ENV_TAURI_FRONTEND_PATH}`"));
+    panic!("Couldn't recognize the {} folder as a Tauri project. It must contain a `{}`, `{}` or `{}` file in any subfolder.",
+      env_var_name.as_deref().unwrap_or("current"),
       ConfigFormat::Json.into_file_name(),
       ConfigFormat::Json5.into_file_name(),
       ConfigFormat::Toml.into_file_name()
     )
-  )).expect("tauri dir already resolved");
+  })).expect("tauri dir already resolved");
   APP_DIR
     .set(resolve_app_dir().unwrap_or_else(|| tauri_dir().parent().unwrap().to_path_buf()))
     .expect("app dir already resolved");
@@ -122,12 +133,13 @@ pub fn tauri_dir() -> &'static PathBuf {
 }
 
 pub fn resolve_app_dir() -> Option<PathBuf> {
-  let cwd = current_dir().expect("failed to read cwd");
-  if cwd.join("package.json").exists() {
-    return Some(cwd);
+  let app_dir = env_tauri_app_path().unwrap_or_else(|| current_dir().expect("failed to read cwd"));
+
+  if app_dir.join("package.json").exists() {
+    return Some(app_dir);
   }
 
-  lookup(&cwd, |path| {
+  lookup(&app_dir, |path| {
     if let Some(file_name) = path.file_name() {
       file_name == OsStr::new("package.json")
     } else {