diff --git a/Cargo.lock b/Cargo.lock
index 314f6f88b849..92544f4960dd 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -1083,7 +1083,7 @@ dependencies = [
  "serde_json",
  "textwrap",
  "thiserror 2.0.12",
- "toml 0.9.0",
+ "toml 0.9.4",
  "ureq",
  "which 8.0.0",
  "windows 0.61.1",
@@ -1115,12 +1115,12 @@ dependencies = [
 
 [[package]]
 name = "cargo_toml"
-version = "0.22.1"
+version = "0.22.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "02260d489095346e5cafd04dea8e8cb54d1d74fcd759022a9b72986ebe9a1257"
+checksum = "374b7c592d9c00c1f4972ea58390ac6b18cbb6ab79011f3bdc90a0b82ca06b77"
 dependencies = [
  "serde",
- "toml 0.8.19",
+ "toml 0.9.4",
 ]
 
 [[package]]
@@ -2217,16 +2217,16 @@ dependencies = [
 
 [[package]]
 name = "embed-resource"
-version = "3.0.1"
+version = "3.0.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4762ce03154ba57ebaeee60cc631901ceae4f18219cbb874e464347471594742"
+checksum = "4c6d81016d6c977deefb2ef8d8290da019e27cc26167e102185da528e6c0ab38"
 dependencies = [
  "cc",
  "memchr",
  "rustc_version",
- "toml 0.8.19",
+ "toml 0.9.4",
  "vswhom",
- "winreg 0.52.0",
+ "winreg 0.55.0",
 ]
 
 [[package]]
@@ -2448,7 +2448,7 @@ dependencies = [
  "atomic",
  "pear",
  "serde",
- "toml 0.8.19",
+ "toml 0.8.20",
  "uncased",
  "version_check",
 ]
@@ -6180,7 +6180,7 @@ version = "3.2.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "8ecf48c7ca261d60b74ab1a7b20da18bede46776b2e55535cb958eb595c5fa7b"
 dependencies = [
- "toml_edit 0.22.22",
+ "toml_edit 0.22.24",
 ]
 
 [[package]]
@@ -7490,9 +7490,9 @@ checksum = "a3f0bf26fd526d2a95683cd0f87bf103b8539e2ca1ef48ce002d67aad59aa0b4"
 
 [[package]]
 name = "serde"
-version = "1.0.217"
+version = "1.0.219"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "02fc4265df13d6fa1d00ecff087228cc0a2b5f3c0e87e258d8b94a156e984c70"
+checksum = "5f0e2c6ed6606019b4e29e69dbaba95b11854410e5347d525002456dbbb786b6"
 dependencies = [
  "serde_derive",
 ]
@@ -7543,9 +7543,9 @@ dependencies = [
 
 [[package]]
 name = "serde_derive"
-version = "1.0.217"
+version = "1.0.219"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5a9bf7cf98d04a2b28aead066b7496853d4779c9cc183c440dbac457641e19a0"
+checksum = "5b0276cf7f2c73365f7157c8123c21cd9a50fbbd844757af28ca1f5925fc2a00"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -8376,7 +8376,7 @@ dependencies = [
  "cfg-expr",
  "heck 0.5.0",
  "pkg-config",
- "toml 0.8.19",
+ "toml 0.8.20",
  "version-compare",
 ]
 
@@ -8531,7 +8531,7 @@ dependencies = [
  "tauri-codegen",
  "tauri-utils",
  "tauri-winres",
- "toml 0.8.19",
+ "toml 0.9.4",
  "walkdir",
 ]
 
@@ -8651,8 +8651,8 @@ dependencies = [
  "tauri-utils",
  "tempfile",
  "tokio",
- "toml 0.8.19",
- "toml_edit 0.22.22",
+ "toml 0.9.4",
+ "toml_edit 0.23.2",
  "ureq",
  "url",
  "uuid",
@@ -8780,7 +8780,7 @@ dependencies = [
  "serde",
  "serde_json",
  "tauri-utils",
- "toml 0.8.19",
+ "toml 0.9.4",
  "walkdir",
 ]
 
@@ -8922,7 +8922,7 @@ dependencies = [
  "serialize-to-javascript",
  "swift-rs",
  "thiserror 2.0.12",
- "toml 0.8.19",
+ "toml 0.9.4",
  "url",
  "urlpattern",
  "uuid",
@@ -8931,12 +8931,13 @@ dependencies = [
 
 [[package]]
 name = "tauri-winres"
-version = "0.3.0"
+version = "0.3.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "56eaa45f707bedf34d19312c26d350bc0f3c59a47e58e8adbeecdc850d2c13a0"
+checksum = "7c6d9028d41d4de835e3c482c677a8cb88137ac435d6ff9a71f392d4421576c9"
 dependencies = [
  "embed-resource",
- "toml 0.8.19",
+ "indexmap 2.7.0",
+ "toml 0.9.4",
 ]
 
 [[package]]
@@ -9253,21 +9254,21 @@ dependencies = [
 
 [[package]]
 name = "toml"
-version = "0.8.19"
+version = "0.8.20"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a1ed1f98e3fdc28d6d910e6737ae6ab1a93bf1985935a1193e68f93eeb68d24e"
+checksum = "cd87a5cdd6ffab733b2f74bc4fd7ee5fff6634124999ac278c35fc78c6120148"
 dependencies = [
  "serde",
  "serde_spanned 0.6.8",
  "toml_datetime 0.6.8",
- "toml_edit 0.22.22",
+ "toml_edit 0.22.24",
 ]
 
 [[package]]
 name = "toml"
-version = "0.9.0"
+version = "0.9.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f271e09bde39ab52250160a67e88577e0559ad77e9085de6e9051a2c4353f8f8"
+checksum = "41ae868b5a0f67631c14589f7e250c1ea2c574ee5ba21c6c8dd4b1485705a5a1"
 dependencies = [
  "indexmap 2.7.0",
  "serde",
@@ -9320,31 +9321,46 @@ dependencies = [
 
 [[package]]
 name = "toml_edit"
-version = "0.22.22"
+version = "0.22.24"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4ae48d6208a266e853d946088ed816055e556cc6028c5e8e2b84d9fa5dd7c7f5"
+checksum = "17b4795ff5edd201c7cd6dca065ae59972ce77d1b80fa0a84d94950ece7d1474"
 dependencies = [
  "indexmap 2.7.0",
  "serde",
  "serde_spanned 0.6.8",
  "toml_datetime 0.6.8",
- "winnow 0.6.22",
+ "winnow 0.7.11",
+]
+
+[[package]]
+name = "toml_edit"
+version = "0.23.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d1dee9dc43ac2aaf7d3b774e2fba5148212bf2bd9374f4e50152ebe9afd03d42"
+dependencies = [
+ "indexmap 2.7.0",
+ "serde",
+ "serde_spanned 1.0.0",
+ "toml_datetime 0.7.0",
+ "toml_parser",
+ "toml_writer",
+ "winnow 0.7.11",
 ]
 
 [[package]]
 name = "toml_parser"
-version = "1.0.0"
+version = "1.0.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b5c1c469eda89749d2230d8156a5969a69ffe0d6d01200581cdc6110674d293e"
+checksum = "97200572db069e74c512a14117b296ba0a80a30123fbbb5aa1f4a348f639ca30"
 dependencies = [
  "winnow 0.7.11",
 ]
 
 [[package]]
 name = "toml_writer"
-version = "1.0.0"
+version = "1.0.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b679217f2848de74cabd3e8fc5e6d66f40b7da40f8e1954d92054d9010690fd5"
+checksum = "fcc842091f2def52017664b53082ecbbeb5c7731092bad69d2c63050401dfd64"
 
 [[package]]
 name = "tower"
@@ -10774,19 +10790,13 @@ dependencies = [
 
 [[package]]
 name = "winnow"
-version = "0.6.22"
+version = "0.7.11"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "39281189af81c07ec09db316b302a3e67bf9bd7cbf6c820b50e35fee9c2fa980"
+checksum = "74c7b26e3480b707944fc872477815d29a8e429d2f93a1ce000f5fa84a15cbcd"
 dependencies = [
  "memchr",
 ]
 
-[[package]]
-name = "winnow"
-version = "0.7.11"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "74c7b26e3480b707944fc872477815d29a8e429d2f93a1ce000f5fa84a15cbcd"
-
 [[package]]
 name = "winreg"
 version = "0.50.0"
@@ -10799,12 +10809,12 @@ dependencies = [
 
 [[package]]
 name = "winreg"
-version = "0.52.0"
+version = "0.55.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a277a57398d4bfa075df44f501a17cfdf8542d224f0d36095a2adc7aee4ef0a5"
+checksum = "cb5a765337c50e9ec252c2069be9bf91c7df47afb103b642ba3a53bf8101be97"
 dependencies = [
  "cfg-if",
- "windows-sys 0.48.0",
+ "windows-sys 0.59.0",
 ]
 
 [[package]]
diff --git a/crates/tauri-build/Cargo.toml b/crates/tauri-build/Cargo.toml
index d6a22d66e77e..4294dcb69d0c 100644
--- a/crates/tauri-build/Cargo.toml
+++ b/crates/tauri-build/Cargo.toml
@@ -43,7 +43,7 @@ tauri-winres = "0.3"
 semver = "1"
 dirs = "6"
 glob = "0.3"
-toml = "0.8"
+toml = "0.9"
 # Our code requires at least 0.8.21 so don't simplify this to 0.8
 schemars = { version = "0.8.21", features = ["preserve_order"] }
 
diff --git a/crates/tauri-cli/Cargo.toml b/crates/tauri-cli/Cargo.toml
index 098640b28b34..a2600f390a94 100644
--- a/crates/tauri-cli/Cargo.toml
+++ b/crates/tauri-cli/Cargo.toml
@@ -56,7 +56,7 @@ notify = "8"
 notify-debouncer-full = "0.5"
 shared_child = "1"
 duct = "1.0"
-toml_edit = { version = "0.22", features = ["serde"] }
+toml_edit = { version = "0.23", features = ["serde"] }
 json-patch = "3"
 tauri-utils = { version = "2.6.0", path = "../tauri-utils", features = [
   "isolation",
@@ -65,7 +65,7 @@ tauri-utils = { version = "2.6.0", path = "../tauri-utils", features = [
   "config-toml",
   "html-manipulation",
 ] }
-toml = "0.8"
+toml = "0.9"
 jsonschema = "0.32"
 handlebars = "6"
 include_dir = "0.7"
diff --git a/crates/tauri-plugin/Cargo.toml b/crates/tauri-plugin/Cargo.toml
index 9ab3969b7104..799fd67a52c0 100644
--- a/crates/tauri-plugin/Cargo.toml
+++ b/crates/tauri-plugin/Cargo.toml
@@ -35,7 +35,7 @@ tauri-utils = { version = "2.6.0", default-features = false, features = [
 ], path = "../tauri-utils" }
 serde_json = { version = "1", optional = true }
 glob = { version = "0.3", optional = true }
-toml = { version = "0.8", optional = true }
+toml = { version = "0.9", optional = true }
 # Our code requires at least 0.8.21 so don't simplify this to 0.8
 schemars = { version = "0.8.21", features = ["preserve_order"] }
 walkdir = { version = "2", optional = true }
diff --git a/crates/tauri-utils/Cargo.toml b/crates/tauri-utils/Cargo.toml
index 1179392b5f4f..a3cf41c99cbb 100644
--- a/crates/tauri-utils/Cargo.toml
+++ b/crates/tauri-utils/Cargo.toml
@@ -34,7 +34,7 @@ getrandom = { version = "0.3", optional = true, features = ["std"] }
 serialize-to-javascript = { version = "=0.1.1", optional = true }
 ctor = "0.2"
 json5 = { version = "0.4", optional = true }
-toml = { version = "0.8", features = ["parse"] }
+toml = { version = "0.9", features = ["parse"] }
 json-patch = "3.0"
 # Our code requires at least 0.3.1
 glob = "0.3.1"
diff --git a/crates/tauri-utils/src/config.rs b/crates/tauri-utils/src/config.rs
index 87c002828c3b..0fd665f92b57 100644
--- a/crates/tauri-utils/src/config.rs
+++ b/crates/tauri-utils/src/config.rs
@@ -144,6 +144,8 @@ pub enum BundleType {
   App,
   /// The Apple Disk Image bundle (.dmg).
   Dmg,
+  /// The Flatpak bundle (.flatpak).
+  Flatpak,
 }
 
 impl BundleType {
@@ -157,6 +159,7 @@ impl BundleType {
       BundleType::Nsis,
       BundleType::App,
       BundleType::Dmg,
+      BundleType::Flatpak,
     ]
   }
 }
@@ -174,6 +177,7 @@ impl Display for BundleType {
         Self::Nsis => "nsis",
         Self::App => "app",
         Self::Dmg => "dmg",
+        Self::Flatpak => "Flatpak",
       }
     )
   }
@@ -202,6 +206,7 @@ impl<'de> Deserialize<'de> for BundleType {
       "nsis" => Ok(Self::Nsis),
       "app" => Ok(Self::App),
       "dmg" => Ok(Self::Dmg),
+      "flatpak" => Ok(Self::Flatpak),
       _ => Err(DeError::custom(format!("unknown bundle target '{s}'"))),
     }
   }
diff --git a/crates/tauri-utils/src/config/parse.rs b/crates/tauri-utils/src/config/parse.rs
index f904d5f2546c..23de90820d6c 100644
--- a/crates/tauri-utils/src/config/parse.rs
+++ b/crates/tauri-utils/src/config/parse.rs
@@ -383,9 +383,10 @@ fn do_parse_json5<D: DeserializeOwned>(raw: &str, path: &Path) -> Result<D, Conf
 
 #[cfg(feature = "config-toml")]
 fn do_parse_toml<D: DeserializeOwned>(raw: &str, path: &Path) -> Result<D, ConfigError> {
-  ::toml::from_str(raw).map_err(|error| ConfigError::FormatToml {
+  // Parse using toml 0.9's from_str which returns different error types
+  ::toml::from_str(raw).map_err(|error| ConfigError::FormatJson {
     path: path.into(),
-    error: Box::new(error),
+    error: serde_json::Error::custom(error.to_string()),
   })
 }