diff --git a/.changes/fix-frontenddir-target-error.md b/.changes/fix-frontenddir-target-error.md
new file mode 100644
index 000000000..4ae48f76c
--- /dev/null
+++ b/.changes/fix-frontenddir-target-error.md
@@ -0,0 +1,6 @@
+---
+"tauri-cli": "patch:bug"
+"@tauri-apps/cli": "patch:bug"
+---
+
+fix: allow the target directory to be inside frontendDir as long as it is not the Rust target directory inside frontendDir.
diff --git a/crates/tauri-cli/src/build.rs b/crates/tauri-cli/src/build.rs
index 87c81b314..f8e77f3d6 100644
--- a/crates/tauri-cli/src/build.rs
+++ b/crates/tauri-cli/src/build.rs
@@ -9,12 +9,12 @@ use crate::{
     app_paths::tauri_dir,
     config::{get as get_config, ConfigHandle, FrontendDist},
   },
-  interface::{AppInterface, Interface},
+  interface::{rust::get_cargo_target_dir, AppInterface, Interface},
   ConfigValue, Result,
 };
 use anyhow::Context;
 use clap::{ArgAction, Parser};
-use std::env::set_current_dir;
+use std::{env::set_current_dir, fs};
 use tauri_utils::platform::Target;
 
 #[derive(Debug, Clone, Parser)]
@@ -172,19 +172,32 @@ pub fn setup(
         ));
     }
 
+    // Issue #13287 - Allow the use of target dir inside frontendDist/distDir
+    // https://github.com/tauri-apps/tauri/issues/13287
+    let target_path = fs::canonicalize(get_cargo_target_dir(&options.args)?)?;
     let mut out_folders = Vec::new();
-    for folder in &["node_modules", "src-tauri", "target"] {
-      if web_asset_path.join(folder).is_dir() {
-        out_folders.push(folder.to_string());
+    if let Ok(web_asset_canonical) = web_asset_path.canonicalize() {
+      if let Ok(relative_path) = target_path.strip_prefix(&web_asset_canonical) {
+        let relative_str = relative_path.to_string_lossy();
+        if !relative_str.is_empty() {
+          out_folders.push(relative_str.to_string());
+        }
+      }
+
+      for folder in &["node_modules", "src-tauri"] {
+        let sub_path = web_asset_canonical.join(folder);
+        if sub_path.is_dir() {
+          out_folders.push(folder.to_string());
+        }
       }
     }
+
     if !out_folders.is_empty() {
       return Err(anyhow::anyhow!(
-          "The configured frontendDist includes the `{:?}` {}. Please isolate your web assets on a separate folder and update `tauri.conf.json > build > frontendDist`.",
-          out_folders,
-          if out_folders.len() == 1 { "folder" } else { "folders" }
-        )
-      );
+        "The configured frontendDist includes the `{:?}` {}. Please isolate your web assets on a separate folder and update `tauri.conf.json > build > frontendDist`.",
+        out_folders,
+        if out_folders.len() == 1 { "folder" } else { "folders" }
+      ));
     }
   }
 
diff --git a/crates/tauri-cli/src/interface/rust.rs b/crates/tauri-cli/src/interface/rust.rs
index 53ba9350a..1638693af 100644
--- a/crates/tauri-cli/src/interface/rust.rs
+++ b/crates/tauri-cli/src/interface/rust.rs
@@ -1148,22 +1148,29 @@ pub(crate) fn get_cargo_metadata() -> crate::Result<CargoMetadata> {
   Ok(serde_json::from_slice(&output.stdout)?)
 }
 
+/// Get the cargo target directory based on the provided arguments.
+/// If "--target-dir" is specified in args, use it as the target directory (relative to current directory).
+/// Otherwise, use the target directory from cargo metadata.
+pub(crate) fn get_cargo_target_dir(args: &[String]) -> crate::Result<PathBuf> {
+  let path = if let Some(target) = get_cargo_option(args, "--target-dir") {
+    std::env::current_dir()?.join(target)
+  } else {
+    get_cargo_metadata()
+      .with_context(|| "failed to get cargo metadata")?
+      .target_directory
+  };
+
+  Ok(path)
+}
+
 /// This function determines the 'target' directory and suffixes it with the profile
 /// to determine where the compiled binary will be located.
 fn get_target_dir(triple: Option<&str>, options: &Options) -> crate::Result<PathBuf> {
-  let mut path = if let Some(target) = get_cargo_option(&options.args, "--target-dir") {
-    std::env::current_dir()?.join(target)
-  } else {
-    let mut path = get_cargo_metadata()
-      .with_context(|| "failed to get cargo metadata")?
-      .target_directory;
+  let mut path = get_cargo_target_dir(&options.args)?;
 
-    if let Some(triple) = triple {
-      path.push(triple);
-    }
-
-    path
-  };
+  if let Some(triple) = triple {
+    path.push(triple);
+  }
 
   path.push(get_profile_dir(options));
 
@@ -1633,7 +1640,10 @@ mod tests {
     );
     assert_eq!(
       get_target_dir(Some("x86_64-pc-windows-msvc"), &options).unwrap(),
-      current_dir.join("path/to/some/dir/release")
+      current_dir
+        .join("path/to/some/dir")
+        .join("x86_64-pc-windows-msvc")
+        .join("release")
     );
 
     let options = Options {