diff --git a/Cargo.lock b/Cargo.lock
index 2db3ed69597e7..98e58bde8bbc8 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -3435,7 +3435,6 @@ dependencies = [
  "ruff_linter",
  "ruff_python_ast",
  "ruff_ranged_value",
- "ruff_source_file",
  "ruff_workspace",
  "salsa",
 ]
diff --git a/crates/ruff/src/diagnostics.rs b/crates/ruff/src/diagnostics.rs
index 8a6535a00997a..61311515bb05a 100644
--- a/crates/ruff/src/diagnostics.rs
+++ b/crates/ruff/src/diagnostics.rs
@@ -225,8 +225,7 @@ pub(crate) fn lint_path(
                         return Ok(Diagnostics::from_source_error(&err, Some(path), settings));
                     }
                 };
-                let source_file = SourceFileBuilder::new(path.to_string_lossy(), contents).finish();
-                lint_pyproject_toml(&source_file, settings)
+                lint_pyproject_toml(path, &contents, settings)
             } else {
                 vec![]
             };
@@ -370,8 +369,6 @@ pub(crate) fn lint_stdin(
             }
 
             let path = path.unwrap();
-            let source_file =
-                SourceFileBuilder::new(path.to_string_lossy(), contents.clone()).finish();
 
             match fix_mode {
                 flags::FixMode::Diff | flags::FixMode::Generate => {}
@@ -379,7 +376,7 @@ pub(crate) fn lint_stdin(
             }
 
             return Ok(Diagnostics {
-                inner: lint_pyproject_toml(&source_file, &settings.linter),
+                inner: lint_pyproject_toml(path, &contents, &settings.linter),
                 fixed: FixMap::from_iter([(fs::relativize_path(path), FixTable::default())]),
                 notebook_indexes: FxHashMap::default(),
             });
diff --git a/crates/ruff_linter/resources/mdtest/ruff/invalid-pyproject-toml.md b/crates/ruff_linter/resources/mdtest/ruff/invalid-pyproject-toml.md
index 47fcd4206bdb0..033ca832e92a1 100644
--- a/crates/ruff_linter/resources/mdtest/ruff/invalid-pyproject-toml.md
+++ b/crates/ruff_linter/resources/mdtest/ruff/invalid-pyproject-toml.md
@@ -5,6 +5,8 @@
 select = ["RUF200"]
 ```
 
+## Reports an invalid `pyproject.toml`
+
 `pyproject.toml`:
 
 ```toml
@@ -20,3 +22,18 @@ error[RUF200]: Failed to parse pyproject.toml: invalid type: integer `1`, expect
   |        ^
   |
 ```
+
+## Respects per-file ignores
+
+```toml
+[lint]
+select = ["RUF200"]
+per-file-ignores = { "pyproject.toml" = ["RUF200"] }
+```
+
+`pyproject.toml`:
+
+```toml
+[project]
+name = 1
+```
diff --git a/crates/ruff_linter/src/checkers/ast/mod.rs b/crates/ruff_linter/src/checkers/ast/mod.rs
index cdfa6c1bc4a78..afdf134f1e0f1 100644
--- a/crates/ruff_linter/src/checkers/ast/mod.rs
+++ b/crates/ruff_linter/src/checkers/ast/mod.rs
@@ -3548,6 +3548,11 @@ impl<'a> LintContext<'a> {
         (self.diagnostics.into_inner(), self.source_file)
     }
 
+    #[inline]
+    pub(crate) fn into_diagnostics(self) -> Vec<Diagnostic> {
+        self.diagnostics.into_inner()
+    }
+
     #[inline]
     pub(crate) fn as_mut_vec(&mut self) -> &mut Vec<Diagnostic> {
         self.diagnostics.get_mut()
diff --git a/crates/ruff_linter/src/pyproject_toml.rs b/crates/ruff_linter/src/pyproject_toml.rs
index 8b319f595cddd..583f099981e68 100644
--- a/crates/ruff_linter/src/pyproject_toml.rs
+++ b/crates/ruff_linter/src/pyproject_toml.rs
@@ -1,61 +1,25 @@
-use colored::Colorize;
-use log::warn;
-use pyproject_toml::PyProjectToml;
-use ruff_text_size::{TextRange, TextSize};
+use std::path::Path;
 
+use pyproject_toml::PyProjectToml;
 use ruff_db::diagnostic::Diagnostic;
-use ruff_source_file::SourceFile;
 
-use crate::registry::Rule;
-use crate::rules::ruff::rules::InvalidPyprojectToml;
+use crate::checkers::ast::LintContext;
+use crate::codes::Rule;
+use crate::rules::ruff::rules::invalid_pyproject_toml;
 use crate::settings::LinterSettings;
-use crate::{IOError, Violation};
 
-/// RUF200
-pub fn lint_pyproject_toml(source_file: &SourceFile, settings: &LinterSettings) -> Vec<Diagnostic> {
-    let Some(err) = toml::from_str::<PyProjectToml>(source_file.source_text()).err() else {
-        return Vec::default();
-    };
+pub fn lint_pyproject_toml(
+    path: &Path,
+    contents: &str,
+    settings: &LinterSettings,
+) -> Vec<Diagnostic> {
+    let context = LintContext::new(path, contents, settings);
 
-    let mut messages = Vec::new();
-    let range = match err.span() {
-        // This is bad but sometimes toml and/or serde just don't give us spans
-        // TODO(konstin,micha): https://github.com/astral-sh/ruff/issues/4571
-        None => TextRange::default(),
-        Some(range) => {
-            let Ok(end) = TextSize::try_from(range.end) else {
-                let message = format!(
-                    "{} is larger than 4GB, but ruff assumes all files to be smaller",
-                    source_file.name(),
-                );
-                if settings.rules.enabled(Rule::IOError) {
-                    let diagnostic =
-                        IOError { message }.into_diagnostic(TextRange::default(), source_file);
-                    messages.push(diagnostic);
-                } else {
-                    warn!(
-                        "{}{}{} {message}",
-                        "Failed to lint ".bold(),
-                        source_file.name().bold(),
-                        ":".bold()
-                    );
-                }
-                return messages;
-            };
-            TextRange::new(
-                // start <= end, so if end < 4GB follows start < 4GB
-                TextSize::try_from(range.start).unwrap(),
-                end,
-            )
+    if let Err(err) = toml::from_str::<PyProjectToml>(contents) {
+        if context.is_rule_enabled(Rule::InvalidPyprojectToml) {
+            invalid_pyproject_toml(&context, &err);
         }
-    };
-
-    if settings.rules.enabled(Rule::InvalidPyprojectToml) {
-        let toml_err = err.message().to_string();
-        let diagnostic =
-            InvalidPyprojectToml { message: toml_err }.into_diagnostic(range, source_file);
-        messages.push(diagnostic);
     }
 
-    messages
+    context.into_diagnostics()
 }
diff --git a/crates/ruff_linter/src/rules/ruff/mod.rs b/crates/ruff_linter/src/rules/ruff/mod.rs
index 68bd7b17265e9..a91f858996dc7 100644
--- a/crates/ruff_linter/src/rules/ruff/mod.rs
+++ b/crates/ruff_linter/src/rules/ruff/mod.rs
@@ -13,7 +13,6 @@ mod tests {
     use anyhow::Result;
     use regex::Regex;
     use ruff_python_ast::PythonVersion;
-    use ruff_source_file::SourceFileBuilder;
     use rustc_hash::FxHashSet;
     use test_case::test_case;
 
@@ -795,9 +794,9 @@ mod tests {
             .join(path)
             .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,
+            Path::new("pyproject.toml"),
+            &contents,
             &settings::LinterSettings::for_rule(Rule::InvalidPyprojectToml),
         );
         assert_diagnostics!(snapshot, messages);
diff --git a/crates/ruff_linter/src/rules/ruff/rules/invalid_pyproject_toml.rs b/crates/ruff_linter/src/rules/ruff/rules/invalid_pyproject_toml.rs
index 4da7ce2996bf9..be78db98cf6e3 100644
--- a/crates/ruff_linter/src/rules/ruff/rules/invalid_pyproject_toml.rs
+++ b/crates/ruff_linter/src/rules/ruff/rules/invalid_pyproject_toml.rs
@@ -1,6 +1,7 @@
 use ruff_macros::{ViolationMetadata, derive_message_formats};
+use ruff_text_size::{TextRange, TextSize};
 
-use crate::{FixAvailability, Violation};
+use crate::{FixAvailability, Violation, checkers::ast::LintContext};
 
 /// ## What it does
 /// Checks for any pyproject.toml that does not conform to the schema from the relevant PEPs.
@@ -45,3 +46,19 @@ impl Violation for InvalidPyprojectToml {
         format!("Failed to parse pyproject.toml: {message}")
     }
 }
+
+/// RUF200
+pub(crate) fn invalid_pyproject_toml(context: &LintContext, err: &toml::de::Error) {
+    let range = match err.span() {
+        // This is bad but sometimes toml and/or serde just don't give us spans
+        // TODO(konstin,micha): https://github.com/astral-sh/ruff/issues/4571
+        None => TextRange::default(),
+        Some(range) => TextRange::new(
+            TextSize::try_from(range.start).unwrap(),
+            TextSize::try_from(range.end).unwrap(),
+        ),
+    };
+
+    let toml_err = err.message().to_string();
+    context.report_diagnostic(InvalidPyprojectToml { message: toml_err }, range);
+}
diff --git a/crates/ruff_mdtest/Cargo.toml b/crates/ruff_mdtest/Cargo.toml
index cbf24ad06a733..9209374fc5a3f 100644
--- a/crates/ruff_mdtest/Cargo.toml
+++ b/crates/ruff_mdtest/Cargo.toml
@@ -20,7 +20,6 @@ ruff_db = { workspace = true, features = ["os", "testing"] }
 ruff_linter = { workspace = true, features = ["testing"] }
 ruff_python_ast = { workspace = true }
 ruff_ranged_value = { workspace = true }
-ruff_source_file = { workspace = true }
 ruff_workspace = { workspace = true }
 
 anyhow = { workspace = true }
diff --git a/crates/ruff_mdtest/src/lib.rs b/crates/ruff_mdtest/src/lib.rs
index 1fbe0b1512638..c35ced5469294 100644
--- a/crates/ruff_mdtest/src/lib.rs
+++ b/crates/ruff_mdtest/src/lib.rs
@@ -15,7 +15,6 @@ use ruff_linter::source_kind::SourceKind;
 use ruff_linter::test::test_contents;
 use ruff_python_ast::SourceType;
 use ruff_ranged_value::{ValueSource, ValueSourceGuard};
-use ruff_source_file::SourceFileBuilder;
 use ruff_workspace::configuration::Configuration;
 use ruff_workspace::options::Options;
 
@@ -128,10 +127,7 @@ fn run_test(
                             test_contents(&source_kind, path, &settings.linter).0
                         }
                         SourceType::Toml(source_type) if source_type.is_pyproject() => {
-                            let source_file =
-                                SourceFileBuilder::new(path.to_string_lossy(), source.as_str())
-                                    .finish();
-                            lint_pyproject_toml(&source_file, &settings.linter)
+                            lint_pyproject_toml(path, source.as_str(), &settings.linter)
                         }
                         SourceType::Toml(_) | SourceType::Markdown => Vec::new(),
                     }