diff --git a/Cargo.lock b/Cargo.lock
index 6d4198b3a..46f2c3716 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -5025,7 +5025,6 @@ dependencies = [
  "serde",
  "thiserror",
  "toml",
- "toml_edit",
  "tracing",
  "uv-cache",
  "uv-fs",
diff --git a/crates/uv-tool/Cargo.toml b/crates/uv-tool/Cargo.toml
index 0fa2adefe..4eae2f0b7 100644
--- a/crates/uv-tool/Cargo.toml
+++ b/crates/uv-tool/Cargo.toml
@@ -28,5 +28,4 @@ tracing = { workspace = true }
 fs-err = { workspace = true }
 serde = { workspace = true }
 toml = { workspace = true } 
-toml_edit = { workspace = true } 
 dirs-sys = { workspace = true }
diff --git a/crates/uv-tool/src/lib.rs b/crates/uv-tool/src/lib.rs
index 85099ac11..ee8f6b96d 100644
--- a/crates/uv-tool/src/lib.rs
+++ b/crates/uv-tool/src/lib.rs
@@ -12,20 +12,21 @@ use uv_cache::Cache;
 use uv_fs::{LockedFile, Simplified};
 use uv_toolchain::{Interpreter, PythonEnvironment};
 
-pub use tools_toml::{Tool, ToolsToml, ToolsTomlMut};
+pub use receipt::ToolReceipt;
+pub use tool::Tool;
 
 use uv_state::{StateBucket, StateStore};
-mod tools_toml;
+mod receipt;
+mod tool;
 
 #[derive(Error, Debug)]
 pub enum Error {
     #[error(transparent)]
     IO(#[from] io::Error),
-    // TODO(zanieb): Improve the error handling here
-    #[error("Failed to update `tools.toml` metadata at {0}")]
-    TomlEdit(PathBuf, #[source] tools_toml::Error),
-    #[error("Failed to read `tools.toml` metadata at {0}")]
-    TomlRead(PathBuf, #[source] Box<toml::de::Error>),
+    #[error("Failed to update `uv-receipt.toml` at {0}")]
+    ReceiptWrite(PathBuf, #[source] Box<toml::ser::Error>),
+    #[error("Failed to read `uv-receipt.toml` at {0}")]
+    ReceiptRead(PathBuf, #[source] Box<toml::de::Error>),
     #[error(transparent)]
     VirtualEnvError(#[from] uv_virtualenv::Error),
     #[error("Failed to read package entry points {0}")]
@@ -36,6 +37,8 @@ pub enum Error {
     NoExecutableDirectory,
     #[error(transparent)]
     EnvironmentError(#[from] uv_toolchain::Error),
+    #[error("Failed to find a receipt for tool `{0}` at {1}")]
+    MissingToolReceipt(String, PathBuf),
 }
 
 /// A collection of uv-managed tools installed on the current system.
@@ -51,7 +54,10 @@ impl InstalledTools {
         Self { root: root.into() }
     }
 
+    /// Create a new [`InstalledTools`] from settings.
+    ///
     /// Prefer, in order:
+    ///
     /// 1. The specific tool directory specified by the user, i.e., `UV_TOOL_DIR`
     /// 2. A directory in the system-appropriate user-level data directory, e.g., `~/.local/uv/tools`
     /// 3. A directory in the local data directory, e.g., `./.uv/tools`
@@ -65,47 +71,74 @@ impl InstalledTools {
         }
     }
 
-    pub fn tools_toml_path(&self) -> PathBuf {
-        self.root.join("tools.toml")
+    /// Return the metadata for all installed tools.
+    pub fn tools(&self) -> Result<Vec<(String, Tool)>, Error> {
+        let _lock = self.acquire_lock();
+        let mut tools = Vec::new();
+        for directory in uv_fs::directories(self.root()) {
+            let name = directory.file_name().unwrap().to_string_lossy().to_string();
+            let path = directory.join("uv-receipt.toml");
+            let contents = match fs_err::read_to_string(&path) {
+                Ok(contents) => contents,
+                // TODO(zanieb): Consider warning on malformed tools instead
+                Err(err) if err.kind() == io::ErrorKind::NotFound => {
+                    return Err(Error::MissingToolReceipt(name.clone(), path.clone()))
+                }
+                Err(err) => return Err(err.into()),
+            };
+            let tool_receipt = ToolReceipt::from_string(contents)
+                .map_err(|err| Error::ReceiptRead(path, Box::new(err)))?;
+            tools.push((name, tool_receipt.tool));
+        }
+        Ok(tools)
     }
 
-    /// Return the toml tracking tools.
-    pub fn toml(&self) -> Result<ToolsToml, Error> {
-        match fs_err::read_to_string(self.tools_toml_path()) {
-            Ok(contents) => Ok(ToolsToml::from_string(contents)
-                .map_err(|err| Error::TomlRead(self.tools_toml_path(), Box::new(err)))?),
-            Err(err) if err.kind() == io::ErrorKind::NotFound => Ok(ToolsToml::default()),
-            Err(err) => Err(err.into()),
+    /// Get the receipt for the given tool.
+    pub fn get_tool_receipt(&self, name: &str) -> Result<Option<Tool>, Error> {
+        let path = self.root.join(name).join("uv-receipt.toml");
+        match ToolReceipt::from_path(&path) {
+            Ok(tool_receipt) => Ok(Some(tool_receipt.tool)),
+            Err(Error::IO(err)) if err.kind() == io::ErrorKind::NotFound => Ok(None),
+            Err(err) => Err(err),
         }
     }
 
-    pub fn toml_mut(&self) -> Result<ToolsTomlMut, Error> {
-        let toml = self.toml()?;
-        ToolsTomlMut::from_toml(&toml).map_err(|err| Error::TomlEdit(self.tools_toml_path(), err))
-    }
-
-    pub fn find_tool_entry(&self, name: &str) -> Result<Option<Tool>, Error> {
-        let toml = self.toml()?;
-        Ok(toml.tools.and_then(|tools| tools.get(name).cloned()))
-    }
-
-    pub fn acquire_lock(&self) -> Result<LockedFile, Error> {
+    /// Lock the tools directory.
+    fn acquire_lock(&self) -> Result<LockedFile, Error> {
         Ok(LockedFile::acquire(
             self.root.join(".lock"),
             self.root.user_display(),
         )?)
     }
 
-    pub fn add_tool_entry(&self, name: &str, tool: &Tool) -> Result<(), Error> {
-        let _lock = self.acquire_lock();
+    /// Lock a tool directory.
+    fn acquire_tool_lock(&self, name: &str) -> Result<LockedFile, Error> {
+        let path = self.root.join(name);
+        Ok(LockedFile::acquire(
+            path.join(".lock"),
+            path.user_display(),
+        )?)
+    }
 
-        let mut toml_mut = self.toml_mut()?;
-        toml_mut
-            .add_tool(name, tool)
-            .map_err(|err| Error::TomlEdit(self.tools_toml_path(), err))?;
+    /// Add a receipt for a tool.
+    ///
+    /// Any existing receipt will be replaced.
+    pub fn add_tool_receipt(&self, name: &str, tool: Tool) -> Result<(), Error> {
+        let _lock = self.acquire_tool_lock(name);
+
+        let tool_receipt = ToolReceipt::from(tool);
+        let path = self.root.join(name).join("uv-receipt.toml");
+
+        debug!(
+            "Adding metadata entry for tool `{name}` at {}",
+            path.user_display()
+        );
+
+        let doc = toml::to_string(&tool_receipt)
+            .map_err(|err| Error::ReceiptWrite(path.clone(), Box::new(err)))?;
 
         // Save the modified `tools.toml`.
-        fs_err::write(self.tools_toml_path(), toml_mut.to_string())?;
+        fs_err::write(&path, doc)?;
 
         Ok(())
     }
@@ -189,6 +222,7 @@ impl InstalledTools {
         Ok(self)
     }
 
+    /// Return the path of the tools directory.
     pub fn root(&self) -> &Path {
         &self.root
     }
diff --git a/crates/uv-tool/src/receipt.rs b/crates/uv-tool/src/receipt.rs
new file mode 100644
index 000000000..abf130a09
--- /dev/null
+++ b/crates/uv-tool/src/receipt.rs
@@ -0,0 +1,51 @@
+use std::path::Path;
+
+use serde::{Deserialize, Serialize};
+
+use crate::Tool;
+
+/// A `uv-receipt.toml` file tracking the installation of a tool.
+#[allow(dead_code)]
+#[derive(Debug, Clone, Serialize, Deserialize)]
+pub struct ToolReceipt {
+    pub(crate) tool: Tool,
+
+    /// The raw unserialized document.
+    #[serde(skip)]
+    pub(crate) raw: String,
+}
+
+impl ToolReceipt {
+    /// Parse a [`ToolReceipt`] from a raw TOML string.
+    pub(crate) fn from_string(raw: String) -> Result<Self, toml::de::Error> {
+        let tool = toml::from_str(&raw)?;
+        Ok(ToolReceipt { raw, ..tool })
+    }
+
+    ///  Read a [`ToolReceipt`] from the given path.
+    pub(crate) fn from_path(path: &Path) -> Result<ToolReceipt, crate::Error> {
+        match fs_err::read_to_string(path) {
+            Ok(contents) => Ok(ToolReceipt::from_string(contents)
+                .map_err(|err| crate::Error::ReceiptRead(path.to_owned(), Box::new(err)))?),
+            Err(err) => Err(err.into()),
+        }
+    }
+}
+
+// Ignore raw document in comparison.
+impl PartialEq for ToolReceipt {
+    fn eq(&self, other: &Self) -> bool {
+        self.tool.eq(&other.tool)
+    }
+}
+
+impl Eq for ToolReceipt {}
+
+impl From<Tool> for ToolReceipt {
+    fn from(tool: Tool) -> Self {
+        ToolReceipt {
+            tool,
+            raw: String::new(),
+        }
+    }
+}
diff --git a/crates/uv-tool/src/tool.rs b/crates/uv-tool/src/tool.rs
new file mode 100644
index 000000000..f5d4e98db
--- /dev/null
+++ b/crates/uv-tool/src/tool.rs
@@ -0,0 +1,25 @@
+use pypi_types::VerbatimParsedUrl;
+use serde::{Deserialize, Serialize};
+
+/// A tool entry.
+#[allow(dead_code)]
+#[derive(Debug, Clone, Serialize, PartialEq, Eq, Deserialize)]
+#[serde(rename_all = "kebab-case")]
+#[cfg_attr(feature = "schemars", derive(schemars::JsonSchema))]
+pub struct Tool {
+    requirements: Vec<pep508_rs::Requirement<VerbatimParsedUrl>>,
+    python: Option<String>,
+}
+
+impl Tool {
+    /// Create a new `Tool`.
+    pub fn new(
+        requirements: Vec<pep508_rs::Requirement<VerbatimParsedUrl>>,
+        python: Option<String>,
+    ) -> Self {
+        Self {
+            requirements,
+            python,
+        }
+    }
+}
diff --git a/crates/uv-tool/src/tools_toml.rs b/crates/uv-tool/src/tools_toml.rs
deleted file mode 100644
index 75d7ecd9c..000000000
--- a/crates/uv-tool/src/tools_toml.rs
+++ /dev/null
@@ -1,119 +0,0 @@
-use pypi_types::VerbatimParsedUrl;
-use serde::{Deserialize, Serialize};
-use std::collections::BTreeMap;
-use std::{fmt, mem};
-use thiserror::Error;
-use toml_edit::{DocumentMut, Item, Table, TomlError, Value};
-
-/// A `tools.toml` with an (optional) `[tools]` section.
-#[allow(dead_code)]
-#[derive(Debug, Clone, Default, Deserialize)]
-pub struct ToolsToml {
-    pub(crate) tools: Option<BTreeMap<String, Tool>>,
-
-    /// The raw unserialized document.
-    #[serde(skip)]
-    pub(crate) raw: String,
-}
-
-impl ToolsToml {
-    /// Parse a `ToolsToml` from a raw TOML string.
-    pub(crate) fn from_string(raw: String) -> Result<Self, toml::de::Error> {
-        let tools = toml::from_str(&raw)?;
-        Ok(ToolsToml { raw, ..tools })
-    }
-}
-
-// Ignore raw document in comparison.
-impl PartialEq for ToolsToml {
-    fn eq(&self, other: &Self) -> bool {
-        self.tools.eq(&other.tools)
-    }
-}
-
-impl Eq for ToolsToml {}
-
-/// A `[[tools]]` entry.
-#[allow(dead_code)]
-#[derive(Debug, Clone, Serialize, PartialEq, Eq, Deserialize)]
-#[serde(rename_all = "kebab-case")]
-#[cfg_attr(feature = "schemars", derive(schemars::JsonSchema))]
-pub struct Tool {
-    requirements: Vec<pep508_rs::Requirement<VerbatimParsedUrl>>,
-    python: Option<String>,
-}
-
-impl Tool {
-    /// Create a new `Tool`.
-    pub fn new(
-        requirements: Vec<pep508_rs::Requirement<VerbatimParsedUrl>>,
-        python: Option<String>,
-    ) -> Self {
-        Self {
-            requirements,
-            python,
-        }
-    }
-}
-
-/// Raw and mutable representation of a `tools.toml`.
-///
-/// This is useful for operations that require editing an existing `tools.toml` while
-/// preserving comments and other structure.
-pub struct ToolsTomlMut {
-    doc: DocumentMut,
-}
-
-#[derive(Error, Debug)]
-pub enum Error {
-    #[error("Failed to parse `tools.toml`")]
-    Parse(#[from] Box<TomlError>),
-    #[error("Failed to serialize `tools.toml`")]
-    Serialize(#[from] Box<toml::ser::Error>),
-    #[error("`tools.toml` is malformed")]
-    MalformedTools,
-}
-
-impl ToolsTomlMut {
-    /// Initialize a `ToolsTomlMut` from a `ToolsToml`.
-    pub fn from_toml(tools: &ToolsToml) -> Result<Self, Error> {
-        Ok(Self {
-            doc: tools.raw.parse().map_err(Box::new)?,
-        })
-    }
-
-    /// Adds a tool to `tools`.
-    pub fn add_tool(&mut self, name: &str, tool: &Tool) -> Result<(), Error> {
-        // Get or create `tools`.
-        let tools = self
-            .doc
-            .entry("tools")
-            .or_insert(Item::Table(Table::new()))
-            .as_table_mut()
-            .ok_or(Error::MalformedTools)?;
-
-        add_tool(name, tool, tools)?;
-
-        Ok(())
-    }
-}
-
-/// Adds a tool to the given `tools` table.
-pub(crate) fn add_tool(name: &str, tool: &Tool, tools: &mut Table) -> Result<(), Error> {
-    // Serialize as an inline table.
-    let mut doc = toml::to_string(tool)
-        .map_err(Box::new)?
-        .parse::<DocumentMut>()
-        .unwrap();
-    let table = mem::take(doc.as_table_mut()).into_inline_table();
-
-    tools.insert(name, Item::Value(Value::InlineTable(table)));
-
-    Ok(())
-}
-
-impl fmt::Display for ToolsTomlMut {
-    fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
-        self.doc.fmt(f)
-    }
-}
diff --git a/crates/uv/src/commands/tool/install.rs b/crates/uv/src/commands/tool/install.rs
index bf8a80183..8b6354724 100644
--- a/crates/uv/src/commands/tool/install.rs
+++ b/crates/uv/src/commands/tool/install.rs
@@ -9,7 +9,7 @@ use itertools::Itertools;
 
 use pep508_rs::Requirement;
 use pypi_types::VerbatimParsedUrl;
-use tracing::{debug, trace};
+use tracing::debug;
 use uv_cache::Cache;
 use uv_client::Connectivity;
 use uv_configuration::{Concurrency, PreviewMode, Reinstall};
@@ -53,9 +53,9 @@ pub(crate) async fn install(
 
     // TODO(zanieb): Figure out the interface here, do we infer the name or do we match the `run --from` interface?
     let from = Requirement::<VerbatimParsedUrl>::from_str(&from)?;
-    let existing_tool_entry = installed_tools.find_tool_entry(&name)?;
+    let existing_tool_receipt = installed_tools.get_tool_receipt(&name)?;
     // TODO(zanieb): Automatically replace an existing tool if the request differs
-    let reinstall_entry_points = if existing_tool_entry.is_some() {
+    let reinstall_entry_points = if existing_tool_receipt.is_some() {
         if force {
             debug!("Replacing existing tool due to `--force` flag.");
             false
@@ -93,7 +93,6 @@ pub(crate) async fn install(
         bail!("Expected at least one requirement")
     };
     let tool = Tool::new(requirements, python.clone());
-    let path = installed_tools.tools_toml_path();
 
     let interpreter = Toolchain::find(
         &python
@@ -138,7 +137,7 @@ pub(crate) async fn install(
 
     // Exit early if we're not supposed to be reinstalling entry points
     // e.g. `--reinstall-package` was used for some dependency
-    if existing_tool_entry.is_some() && !reinstall_entry_points {
+    if existing_tool_receipt.is_some() && !reinstall_entry_points {
         writeln!(printer.stderr(), "Updated environment for tool `{name}`")?;
         return Ok(ExitStatus::Success);
     }
@@ -214,18 +213,16 @@ pub(crate) async fn install(
         #[cfg(windows)]
         fs_err::copy(path, target).context("Failed to install entrypoint")?;
     }
+
+    debug!("Adding receipt for tool `{name}`",);
+    let installed_tools = installed_tools.init()?;
+    installed_tools.add_tool_receipt(&name, tool)?;
+
     writeln!(
         printer.stdout(),
         "Installed: {}",
         targets.iter().map(|(name, _, _)| name).join(", ")
     )?;
 
-    trace!(
-        "Tracking installed tool `{name}` in tool metadata at `{}`",
-        path.user_display()
-    );
-    let installed_tools = installed_tools.init()?;
-    installed_tools.add_tool_entry(&name, &tool)?;
-
     Ok(ExitStatus::Success)
 }
diff --git a/crates/uv/tests/tool_install.rs b/crates/uv/tests/tool_install.rs
index e06208287..0d4252788 100644
--- a/crates/uv/tests/tool_install.rs
+++ b/crates/uv/tests/tool_install.rs
@@ -44,7 +44,8 @@ fn tool_install() {
 
     tool_dir.child("black").assert(predicate::path::is_dir());
     tool_dir
-        .child("tools.toml")
+        .child("black")
+        .child("uv-receipt.toml")
         .assert(predicate::path::exists());
 
     let executable = bin_dir.child(format!("black{}", std::env::consts::EXE_SUFFIX));
@@ -72,10 +73,10 @@ fn tool_install() {
     insta::with_settings!({
         filters => context.filters(),
     }, {
-        // We should have a tool entry
-        assert_snapshot!(fs_err::read_to_string(tool_dir.join("tools.toml")).unwrap(), @r###"
-        [tools]
-        black = { requirements = ["black"] }
+        // We should have a tool receipt
+        assert_snapshot!(fs_err::read_to_string(tool_dir.join("black").join("uv-receipt.toml")).unwrap(), @r###"
+        [tool]
+        requirements = ["black"]
         "###);
     });
 
@@ -149,11 +150,10 @@ fn tool_install() {
     insta::with_settings!({
         filters => context.filters(),
     }, {
-        // We should have an additional tool entry
-        assert_snapshot!(fs_err::read_to_string(tool_dir.join("tools.toml")).unwrap(), @r###"
-        [tools]
-        black = { requirements = ["black"] }
-        flask = { requirements = ["flask"] }
+        // We should have a new tool receipt
+        assert_snapshot!(fs_err::read_to_string(tool_dir.join("flask").join("uv-receipt.toml")).unwrap(), @r###"
+        [tool]
+        requirements = ["flask"]
         "###);
     });
 }
@@ -197,7 +197,8 @@ fn tool_install_already_installed() {
 
     tool_dir.child("black").assert(predicate::path::is_dir());
     tool_dir
-        .child("tools.toml")
+        .child("black")
+        .child("uv-receipt.toml")
         .assert(predicate::path::exists());
 
     let executable = bin_dir.child(format!("black{}", std::env::consts::EXE_SUFFIX));
@@ -225,10 +226,10 @@ fn tool_install_already_installed() {
     insta::with_settings!({
         filters => context.filters(),
     }, {
-        // We should have a tool entry
-        assert_snapshot!(fs_err::read_to_string(tool_dir.join("tools.toml")).unwrap(), @r###"
-        [tools]
-        black = { requirements = ["black"] }
+        // We should have a tool receipt
+        assert_snapshot!(fs_err::read_to_string(tool_dir.join("black").join("uv-receipt.toml")).unwrap(), @r###"
+        [tool]
+        requirements = ["black"]
         "###);
     });
 
@@ -254,10 +255,10 @@ fn tool_install_already_installed() {
     insta::with_settings!({
         filters => context.filters(),
     }, {
-        // We should not have an additional tool entry
-        assert_snapshot!(fs_err::read_to_string(tool_dir.join("tools.toml")).unwrap(), @r###"
-        [tools]
-        black = { requirements = ["black"] }
+        // We should not have an additional tool receipt
+        assert_snapshot!(fs_err::read_to_string(tool_dir.join("black").join("uv-receipt.toml")).unwrap(), @r###"
+        [tool]
+        requirements = ["black"]
         "###);
     });
 
@@ -378,7 +379,7 @@ fn tool_install_entry_point_exists() {
     assert!(!tool_dir.child("black").exists());
 
     // We should not write a tools entry
-    assert!(!tool_dir.join("tools.toml").exists());
+    assert!(!tool_dir.join("black").join("uv-receipt.toml").exists());
 
     insta::with_settings!({
         filters => context.filters(),
@@ -480,10 +481,10 @@ fn tool_install_entry_point_exists() {
     insta::with_settings!({
         filters => context.filters(),
     }, {
-        // We write a tool entry
-        assert_snapshot!(fs_err::read_to_string(tool_dir.join("tools.toml")).unwrap(), @r###"
-        [tools]
-        black = { requirements = ["black"] }
+        // We write a tool receipt
+        assert_snapshot!(fs_err::read_to_string(tool_dir.join("black").join("uv-receipt.toml")).unwrap(), @r###"
+        [tool]
+        requirements = ["black"]
         "###);
     });
 
@@ -509,10 +510,10 @@ fn tool_install_entry_point_exists() {
     insta::with_settings!({
         filters => context.filters(),
     }, {
-        // We should have a tool entry
-        assert_snapshot!(fs_err::read_to_string(tool_dir.join("tools.toml")).unwrap(), @r###"
-        [tools]
-        black = { requirements = ["black"] }
+        // We should have a tool receipt
+        assert_snapshot!(fs_err::read_to_string(tool_dir.join("black").join("uv-receipt.toml")).unwrap(), @r###"
+        [tool]
+        requirements = ["black"]
         "###);
     });