diff --git a/crates/ruff/src/pyproject_toml.rs b/crates/ruff/src/pyproject_toml.rs
index cabdff1b39..a0cfeb961b 100644
--- a/crates/ruff/src/pyproject_toml.rs
+++ b/crates/ruff/src/pyproject_toml.rs
@@ -7,7 +7,9 @@ use ruff_diagnostics::Diagnostic;
 use ruff_python_ast::source_code::SourceFile;
 
 use crate::message::Message;
+use crate::registry::Rule;
 use crate::rules::ruff::rules::InvalidPyprojectToml;
+use crate::settings::Settings;
 use crate::IOError;
 
 /// Unlike [`pyproject_toml::PyProjectToml`], in our case `build_system` is also optional
@@ -20,9 +22,11 @@ struct PyProjectToml {
     project: Option<Project>,
 }
 
-pub fn lint_pyproject_toml(source_file: SourceFile) -> Result<Vec<Message>> {
+pub fn lint_pyproject_toml(source_file: SourceFile, settings: &Settings) -> Result<Vec<Message>> {
+    let mut messages = vec![];
+
     let err = match toml::from_str::<PyProjectToml>(source_file.source_text()) {
-        Ok(_) => return Ok(Vec::default()),
+        Ok(_) => return Ok(messages),
         Err(err) => err,
     };
 
@@ -32,17 +36,20 @@ pub fn lint_pyproject_toml(source_file: SourceFile) -> Result<Vec<Message>> {
         None => TextRange::default(),
         Some(range) => {
             let Ok(end) = TextSize::try_from(range.end) else {
-                let diagnostic = Diagnostic::new(
-                    IOError {
-                        message: "pyproject.toml is larger than 4GB".to_string(),
-                    },
-                    TextRange::default(),
-                );
-                return Ok(vec![Message::from_diagnostic(
-                    diagnostic,
-                    source_file,
-                    TextSize::default(),
-                )]);
+                if settings.rules.enabled(Rule::IOError) {
+                    let diagnostic = Diagnostic::new(
+                        IOError {
+                            message: "pyproject.toml is larger than 4GB".to_string(),
+                        },
+                        TextRange::default(),
+                    );
+                    messages.push(Message::from_diagnostic(
+                        diagnostic,
+                        source_file,
+                        TextSize::default(),
+                    ));
+                }
+                return Ok(messages);
             };
             TextRange::new(
                 // start <= end, so if end < 4GB follows start < 4GB
@@ -52,11 +59,15 @@ pub fn lint_pyproject_toml(source_file: SourceFile) -> Result<Vec<Message>> {
         }
     };
 
-    let toml_err = err.message().to_string();
-    let diagnostic = Diagnostic::new(InvalidPyprojectToml { message: toml_err }, range);
-    Ok(vec![Message::from_diagnostic(
-        diagnostic,
-        source_file,
-        TextSize::default(),
-    )])
+    if settings.rules.enabled(Rule::InvalidPyprojectToml) {
+        let toml_err = err.message().to_string();
+        let diagnostic = Diagnostic::new(InvalidPyprojectToml { message: toml_err }, range);
+        messages.push(Message::from_diagnostic(
+            diagnostic,
+            source_file,
+            TextSize::default(),
+        ));
+    }
+
+    Ok(messages)
 }
diff --git a/crates/ruff/src/registry.rs b/crates/ruff/src/registry.rs
index 56e30db0ff..a6ac161b7b 100644
--- a/crates/ruff/src/registry.rs
+++ b/crates/ruff/src/registry.rs
@@ -252,6 +252,7 @@ pub enum LintSource {
     Imports,
     Noqa,
     Filesystem,
+    PyprojectToml,
 }
 
 impl Rule {
@@ -259,6 +260,7 @@ impl Rule {
     /// physical lines).
     pub const fn lint_source(&self) -> LintSource {
         match self {
+            Rule::InvalidPyprojectToml => LintSource::PyprojectToml,
             Rule::UnusedNOQA => LintSource::Noqa,
             Rule::BlanketNOQA
             | Rule::BlanketTypeIgnore
diff --git a/crates/ruff/src/rules/ruff/mod.rs b/crates/ruff/src/rules/ruff/mod.rs
index a110328a24..336a65c7e1 100644
--- a/crates/ruff/src/rules/ruff/mod.rs
+++ b/crates/ruff/src/rules/ruff/mod.rs
@@ -203,7 +203,10 @@ mod tests {
             .join("pyproject.toml");
         let contents = fs::read_to_string(path)?;
         let source_file = SourceFileBuilder::new("pyproject.toml", contents).finish();
-        let messages = lint_pyproject_toml(source_file)?;
+        let messages = lint_pyproject_toml(
+            source_file,
+            &settings::Settings::for_rule(Rule::InvalidPyprojectToml),
+        )?;
         assert_messages!(snapshot, messages);
         Ok(())
     }
diff --git a/crates/ruff_cli/src/diagnostics.rs b/crates/ruff_cli/src/diagnostics.rs
index fe638ad169..f994b7a055 100644
--- a/crates/ruff_cli/src/diagnostics.rs
+++ b/crates/ruff_cli/src/diagnostics.rs
@@ -127,11 +127,20 @@ pub(crate) fn lint_path(
 
     debug!("Checking: {}", path.display());
 
-    // We have to special case this here since the python tokenizer doesn't work with toml
+    // We have to special case this here since the Python tokenizer doesn't work with TOML.
     if is_project_toml(path) {
-        let contents = std::fs::read_to_string(path)?;
-        let source_file = SourceFileBuilder::new(path.to_string_lossy(), contents).finish();
-        let messages = lint_pyproject_toml(source_file)?;
+        let messages = if settings
+            .lib
+            .rules
+            .iter_enabled()
+            .any(|rule_code| rule_code.lint_source().is_pyproject_toml())
+        {
+            let contents = std::fs::read_to_string(path)?;
+            let source_file = SourceFileBuilder::new(path.to_string_lossy(), contents).finish();
+            lint_pyproject_toml(source_file, &settings.lib)?
+        } else {
+            vec![]
+        };
         return Ok(Diagnostics {
             messages,
             ..Diagnostics::default()