diff --git a/crates/ruff/src/commands/add_noqa.rs b/crates/ruff/src/commands/add_noqa.rs
index 928c5ce03e5b3..f46deeecf1e55 100644
--- a/crates/ruff/src/commands/add_noqa.rs
+++ b/crates/ruff/src/commands/add_noqa.rs
@@ -11,7 +11,7 @@ use ruff_linter::source_kind::SourceKind;
 use ruff_linter::warn_user_once;
 use ruff_python_ast::{PySourceType, SourceType};
 use ruff_workspace::resolver::{
-    PyprojectConfig, ResolvedFile, match_exclusion, python_files_in_path,
+    PyprojectConfig, ResolvedFile, match_exclusion, project_files_in_path,
 };
 
 use crate::args::ConfigArguments;
@@ -25,10 +25,22 @@ pub(crate) fn add_noqa(
 ) -> Result<usize> {
     // Collect all the files to check.
     let start = Instant::now();
-    let (paths, resolver) = python_files_in_path(files, pyproject_config, config_arguments)?;
+    let (mut paths, resolver) = project_files_in_path(files, pyproject_config, config_arguments)?;
     let duration = start.elapsed();
     debug!("Identified files to lint in: {duration:?}");
 
+    // Filter out paths for file types not supported for linting
+    paths.retain(|path| {
+        if let Ok(ResolvedFile::Root(path) | ResolvedFile::Nested(path)) = path {
+            matches!(
+                SourceType::from(path),
+                SourceType::Python(PySourceType::Python | PySourceType::Stub)
+            )
+        } else {
+            true
+        }
+    });
+
     if paths.is_empty() {
         warn_user_once!("No Python files found under the given path(s)");
         return Ok(0);
@@ -48,11 +60,7 @@ pub(crate) fn add_noqa(
         .par_iter()
         .flatten()
         .filter_map(|resolved_file| {
-            let SourceType::Python(source_type @ (PySourceType::Python | PySourceType::Stub)) =
-                SourceType::from(resolved_file.path())
-            else {
-                return None;
-            };
+            let source_type = SourceType::from(resolved_file.path());
             let path = resolved_file.path();
             let package = resolved_file
                 .path()
@@ -69,7 +77,7 @@ pub(crate) fn add_noqa(
             {
                 return None;
             }
-            let source_kind = match SourceKind::from_path(path, SourceType::Python(source_type)) {
+            let source_kind = match SourceKind::from_path(path, source_type) {
                 Ok(Some(source_kind)) => source_kind,
                 Ok(None) => return None,
                 Err(e) => {
@@ -81,7 +89,7 @@ pub(crate) fn add_noqa(
                 path,
                 package,
                 &source_kind,
-                source_type,
+                source_type.expect_python(),
                 &settings.linter,
                 reason,
             ) {
diff --git a/crates/ruff/src/commands/analyze_graph.rs b/crates/ruff/src/commands/analyze_graph.rs
index e36173c129715..968dac4c355a2 100644
--- a/crates/ruff/src/commands/analyze_graph.rs
+++ b/crates/ruff/src/commands/analyze_graph.rs
@@ -11,7 +11,7 @@ use ruff_linter::package::PackageRoot;
 use ruff_linter::source_kind::SourceKind;
 use ruff_linter::{warn_user, warn_user_once};
 use ruff_python_ast::SourceType;
-use ruff_workspace::resolver::{ResolvedFile, match_exclusion, python_files_in_path};
+use ruff_workspace::resolver::{ResolvedFile, match_exclusion, project_files_in_path};
 use rustc_hash::{FxBuildHasher, FxHashMap};
 use std::io::Write;
 use std::path::{Path, PathBuf};
@@ -35,7 +35,16 @@ pub(crate) fn analyze_graph(
 
     // Find all Python files.
     let files = resolve_default_files(args.files, false);
-    let (paths, resolver) = python_files_in_path(&files, &pyproject_config, config_arguments)?;
+    let (mut paths, resolver) = project_files_in_path(&files, &pyproject_config, config_arguments)?;
+
+    // Filter to only Python files
+    paths.retain(|path| {
+        if let Ok(ResolvedFile::Root(path) | ResolvedFile::Nested(path)) = path {
+            matches!(SourceType::from(path), SourceType::Python(_))
+        } else {
+            true
+        }
+    });
 
     if paths.is_empty() {
         warn_user_once!("No Python files found under the given path(s)");
@@ -124,6 +133,7 @@ pub(crate) fn analyze_graph(
                 let string_imports = settings.analyze.string_imports;
                 let include_dependencies = settings.analyze.include_dependencies.get(path).cloned();
                 let type_checking_imports = settings.analyze.type_checking_imports;
+                let source_type = settings.analyze.extension.get_source_type(path);
 
                 // Skip excluded files.
                 if (settings.file_resolver.force_exclude || !resolved_file.is_root())
@@ -136,19 +146,6 @@ pub(crate) fn analyze_graph(
                     continue;
                 }
 
-                // Ignore non-Python files.
-                let source_type = match settings.analyze.extension.get_source_type(path) {
-                    SourceType::Python(source_type) => source_type,
-                    SourceType::Toml(_) => {
-                        debug!("Ignoring TOML file: {}", path.display());
-                        continue;
-                    }
-                    SourceType::Markdown => {
-                        debug!("Ignoring Markdown file: {}", path.display());
-                        continue;
-                    }
-                };
-
                 // Convert to system paths.
                 let Ok(package) = package.map(SystemPathBuf::from_path_buf).transpose() else {
                     warn!("Failed to convert package to system path");
@@ -165,10 +162,7 @@ pub(crate) fn analyze_graph(
                 let result = inner_result.clone();
                 scope.spawn(move |_| {
                     // Extract source code (handles both .py and .ipynb files)
-                    let source_kind = match SourceKind::from_path(
-                        path.as_std_path(),
-                        SourceType::Python(source_type),
-                    ) {
+                    let source_kind = match SourceKind::from_path(path.as_std_path(), source_type) {
                         Ok(Some(source_kind)) => source_kind,
                         Ok(None) => {
                             debug!("Skipping non-Python notebook: {path}");
@@ -186,7 +180,7 @@ pub(crate) fn analyze_graph(
                     let mut imports = ModuleImports::detect(
                         &db,
                         source_code,
-                        source_type,
+                        source_type.expect_python(),
                         &path,
                         package.as_deref(),
                         string_imports,
diff --git a/crates/ruff/src/commands/check.rs b/crates/ruff/src/commands/check.rs
index 694b1eb8f2ad7..5a80e4f5ac3b2 100644
--- a/crates/ruff/src/commands/check.rs
+++ b/crates/ruff/src/commands/check.rs
@@ -10,6 +10,7 @@ use log::{debug, warn};
 #[cfg(not(target_family = "wasm"))]
 use rayon::prelude::*;
 use ruff_linter::message::create_panic_diagnostic;
+use ruff_python_ast::{SourceType, TomlSourceType};
 use rustc_hash::FxHashMap;
 
 use ruff_db::diagnostic::Diagnostic;
@@ -22,7 +23,7 @@ use ruff_linter::{IOError, Violation, fs, warn_user_once};
 use ruff_source_file::SourceFileBuilder;
 use ruff_text_size::TextRange;
 use ruff_workspace::resolver::{
-    PyprojectConfig, ResolvedFile, match_exclusion, python_files_in_path,
+    PyprojectConfig, ResolvedFile, match_exclusion, project_files_in_path,
 };
 
 use crate::args::ConfigArguments;
@@ -41,9 +42,21 @@ pub(crate) fn check(
 ) -> Result<Diagnostics> {
     // Collect all the Python files to check.
     let start = Instant::now();
-    let (paths, resolver) = python_files_in_path(files, pyproject_config, config_arguments)?;
+    let (mut paths, resolver) = project_files_in_path(files, pyproject_config, config_arguments)?;
     debug!("Identified files to lint in: {:?}", start.elapsed());
 
+    // Filter out paths for file types not supported for linting
+    paths.retain(|path| {
+        if let Ok(ResolvedFile::Root(path) | ResolvedFile::Nested(path)) = path {
+            matches!(
+                SourceType::from(path),
+                SourceType::Python(_) | SourceType::Toml(TomlSourceType::Pyproject)
+            )
+        } else {
+            true
+        }
+    });
+
     if paths.is_empty() {
         warn_user_once!("No Python files found under the given path(s)");
         return Ok(Diagnostics::default());
diff --git a/crates/ruff/src/commands/check_stdin.rs b/crates/ruff/src/commands/check_stdin.rs
index f76b3ab2df69e..0df58a806031b 100644
--- a/crates/ruff/src/commands/check_stdin.rs
+++ b/crates/ruff/src/commands/check_stdin.rs
@@ -5,7 +5,7 @@ use ruff_db::diagnostic::Diagnostic;
 use ruff_linter::package::PackageRoot;
 use ruff_linter::packaging;
 use ruff_linter::settings::flags;
-use ruff_workspace::resolver::{PyprojectConfig, Resolver, match_exclusion, python_file_at_path};
+use ruff_workspace::resolver::{PyprojectConfig, Resolver, match_exclusion, project_file_at_path};
 
 use crate::args::ConfigArguments;
 use crate::diagnostics::{Diagnostics, lint_stdin};
@@ -23,7 +23,7 @@ pub(crate) fn check_stdin(
 
     if resolver.force_exclude() {
         if let Some(filename) = filename {
-            if !python_file_at_path(filename, &mut resolver, overrides)? {
+            if !project_file_at_path(filename, &mut resolver, overrides)? {
                 if fix_mode.is_apply() {
                     parrot_stdin()?;
                 }
diff --git a/crates/ruff/src/commands/format.rs b/crates/ruff/src/commands/format.rs
index 868493caf6bf6..fdf593d0c5393 100644
--- a/crates/ruff/src/commands/format.rs
+++ b/crates/ruff/src/commands/format.rs
@@ -38,7 +38,7 @@ use ruff_source_file::{LineIndex, LineRanges, OneIndexed, SourceFileBuilder};
 use ruff_text_size::{TextLen, TextRange, TextSize};
 use ruff_workspace::FormatterSettings;
 use ruff_workspace::resolver::{
-    PyprojectConfig, ResolvedFile, Resolver, match_exclusion, python_files_in_path,
+    PyprojectConfig, ResolvedFile, Resolver, match_exclusion, project_files_in_path,
 };
 
 use crate::args::{ConfigArguments, FormatArguments, FormatRange};
@@ -75,7 +75,7 @@ pub(crate) fn format(
 ) -> Result<ExitStatus> {
     let mode = FormatMode::from_cli(&cli);
     let files = resolve_default_files(cli.files, false);
-    let (paths, resolver) = python_files_in_path(&files, pyproject_config, config_arguments)?;
+    let (paths, resolver) = project_files_in_path(&files, pyproject_config, config_arguments)?;
 
     let output_format = pyproject_config.settings.output_format;
     let preview = pyproject_config.settings.formatter.preview;
diff --git a/crates/ruff/src/commands/format_stdin.rs b/crates/ruff/src/commands/format_stdin.rs
index aba5e31cbc26b..e75dd64b1fb79 100644
--- a/crates/ruff/src/commands/format_stdin.rs
+++ b/crates/ruff/src/commands/format_stdin.rs
@@ -7,7 +7,7 @@ use log::error;
 use ruff_linter::source_kind::{SourceError, SourceKind};
 use ruff_python_ast::SourceType;
 use ruff_workspace::FormatterSettings;
-use ruff_workspace::resolver::{PyprojectConfig, Resolver, match_exclusion, python_file_at_path};
+use ruff_workspace::resolver::{PyprojectConfig, Resolver, match_exclusion, project_file_at_path};
 
 use crate::ExitStatus;
 use crate::args::{ConfigArguments, FormatArguments, FormatRange};
@@ -30,7 +30,7 @@ pub(crate) fn format_stdin(
 
     if resolver.force_exclude() {
         if let Some(filename) = cli.stdin_filename.as_deref() {
-            if !python_file_at_path(filename, &mut resolver, config_arguments)? {
+            if !project_file_at_path(filename, &mut resolver, config_arguments)? {
                 if mode.is_write() {
                     parrot_stdin()?;
                 }
diff --git a/crates/ruff/src/commands/show_files.rs b/crates/ruff/src/commands/show_files.rs
index 7c74837fd3495..22826dbd0d5b9 100644
--- a/crates/ruff/src/commands/show_files.rs
+++ b/crates/ruff/src/commands/show_files.rs
@@ -5,7 +5,8 @@ use anyhow::Result;
 use itertools::Itertools;
 
 use ruff_linter::warn_user_once;
-use ruff_workspace::resolver::{PyprojectConfig, ResolvedFile, python_files_in_path};
+use ruff_python_ast::{SourceType, TomlSourceType};
+use ruff_workspace::resolver::{PyprojectConfig, ResolvedFile, project_files_in_path};
 
 use crate::args::ConfigArguments;
 
@@ -17,7 +18,19 @@ pub(crate) fn show_files(
     writer: &mut impl Write,
 ) -> Result<()> {
     // Collect all files in the hierarchy.
-    let (paths, _resolver) = python_files_in_path(files, pyproject_config, config_arguments)?;
+    let (mut paths, _resolver) = project_files_in_path(files, pyproject_config, config_arguments)?;
+
+    // Filter out paths for file types not supported for linting
+    paths.retain(|path| {
+        if let Ok(ResolvedFile::Root(path) | ResolvedFile::Nested(path)) = path {
+            matches!(
+                SourceType::from(path),
+                SourceType::Python(_) | SourceType::Toml(TomlSourceType::Pyproject)
+            )
+        } else {
+            true
+        }
+    });
 
     if paths.is_empty() {
         warn_user_once!("No Python files found under the given path(s)");
diff --git a/crates/ruff/src/commands/show_settings.rs b/crates/ruff/src/commands/show_settings.rs
index 8c38285955e7f..ccea749ae20a7 100644
--- a/crates/ruff/src/commands/show_settings.rs
+++ b/crates/ruff/src/commands/show_settings.rs
@@ -4,7 +4,7 @@ use std::path::PathBuf;
 use anyhow::{Result, bail};
 use itertools::Itertools;
 
-use ruff_workspace::resolver::{PyprojectConfig, ResolvedFile, python_files_in_path};
+use ruff_workspace::resolver::{PyprojectConfig, ResolvedFile, project_files_in_path};
 
 use crate::args::ConfigArguments;
 
@@ -16,7 +16,7 @@ pub(crate) fn show_settings(
     writer: &mut impl Write,
 ) -> Result<()> {
     // Collect all files in the hierarchy.
-    let (paths, resolver) = python_files_in_path(files, pyproject_config, config_arguments)?;
+    let (paths, resolver) = project_files_in_path(files, pyproject_config, config_arguments)?;
 
     // Print the list of files.
     let Some(path) = paths
diff --git a/crates/ruff/tests/cli/snapshots/cli__lint__requires_python_no_tool_preview_enabled.snap b/crates/ruff/tests/cli/snapshots/cli__lint__requires_python_no_tool_preview_enabled.snap
index 885ea0a77fa49..3ada1e2365f76 100644
--- a/crates/ruff/tests/cli/snapshots/cli__lint__requires_python_no_tool_preview_enabled.snap
+++ b/crates/ruff/tests/cli/snapshots/cli__lint__requires_python_no_tool_preview_enabled.snap
@@ -63,6 +63,7 @@ file_resolver.include = [
 	"*.pyw",
 	"*.ipynb",
 	"**/pyproject.toml",
+	"*.md",
 ]
 file_resolver.extend_include = []
 file_resolver.respect_gitignore = true
diff --git a/crates/ruff_dev/src/format_dev.rs b/crates/ruff_dev/src/format_dev.rs
index 82932e76fc7e3..0f25e87bc3553 100644
--- a/crates/ruff_dev/src/format_dev.rs
+++ b/crates/ruff_dev/src/format_dev.rs
@@ -36,7 +36,7 @@ use ruff_python_formatter::{
     FormatModuleError, MagicTrailingComma, PreviewMode, PyFormatOptions, format_module_source,
 };
 use ruff_python_parser::ParseError;
-use ruff_workspace::resolver::{PyprojectConfig, ResolvedFile, Resolver, python_files_in_path};
+use ruff_workspace::resolver::{PyprojectConfig, ResolvedFile, Resolver, project_files_in_path};
 
 fn parse_cli(dirs: &[PathBuf]) -> anyhow::Result<(FormatArguments, ConfigArguments)> {
     let args_matches = FormatCommand::command()
@@ -68,7 +68,7 @@ fn ruff_check_paths<'a>(
     cli: &FormatArguments,
     config_arguments: &ConfigArguments,
 ) -> anyhow::Result<(Vec<Result<ResolvedFile, ignore::Error>>, Resolver<'a>)> {
-    let (paths, resolver) = python_files_in_path(&cli.files, pyproject_config, config_arguments)?;
+    let (paths, resolver) = project_files_in_path(&cli.files, pyproject_config, config_arguments)?;
     Ok((paths, resolver))
 }
 
diff --git a/crates/ruff_workspace/src/options.rs b/crates/ruff_workspace/src/options.rs
index 0f8697445ec9d..bc6339c5c4a7b 100644
--- a/crates/ruff_workspace/src/options.rs
+++ b/crates/ruff_workspace/src/options.rs
@@ -262,7 +262,7 @@ pub struct Options {
     ///
     /// For more information on the glob syntax, refer to the [`globset` documentation](https://docs.rs/globset/latest/globset/#syntax).
     #[option(
-        default = r#"["*.py", "*.pyi", "*.pyw", "*.ipynb", "**/pyproject.toml"]"#,
+        default = r#"["*.py", "*.pyi", "*.pyw", "*.ipynb", "*.md", "**/pyproject.toml"]"#,
         value_type = "list[str]",
         example = r#"
             include = ["*.py"]
diff --git a/crates/ruff_workspace/src/resolver.rs b/crates/ruff_workspace/src/resolver.rs
index c253d3fc83e2b..0dfb203aad2ff 100644
--- a/crates/ruff_workspace/src/resolver.rs
+++ b/crates/ruff_workspace/src/resolver.rs
@@ -432,8 +432,8 @@ impl From<ConfigurationOrigin> for Relativity {
     }
 }
 
-/// Find all Python (`.py`, `.pyi`, `.pyw`, and `.ipynb` files) in a set of paths.
-pub fn python_files_in_path<'a>(
+/// Find all project files in a set of paths, following configured include/exclude settings.
+pub fn project_files_in_path<'a>(
     paths: &[PathBuf],
     pyproject_config: &'a PyprojectConfig,
     transformer: &(dyn ConfigurationTransformer + Sync),
@@ -504,7 +504,7 @@ pub fn python_files_in_path<'a>(
 
     let walker = builder.build_parallel();
 
-    // Run the `WalkParallel` to collect all Python files.
+    // Run the `WalkParallel` to collect all files.
     let state = WalkPythonFilesState::new(resolver);
     let mut visitor = PythonFilesVisitorBuilder::new(transformer, &state);
     walker.visit(&mut visitor);
@@ -762,7 +762,7 @@ impl ResolvedFile {
 }
 
 /// Return `true` if the Python file at [`Path`] is _not_ excluded.
-pub fn python_file_at_path(
+pub fn project_file_at_path(
     path: &Path,
     resolver: &mut Resolver,
     transformer: &dyn ConfigurationTransformer,
@@ -962,7 +962,7 @@ mod tests {
     use crate::pyproject::find_settings_toml;
     use crate::resolver::{
         ConfigurationOrigin, ConfigurationTransformer, PyprojectConfig, PyprojectDiscoveryStrategy,
-        ResolvedFile, Resolver, is_file_excluded, match_exclusion, python_files_in_path,
+        ResolvedFile, Resolver, is_file_excluded, match_exclusion, project_files_in_path,
         resolve_root_settings,
     };
     use crate::settings::Settings;
@@ -1024,7 +1024,7 @@ mod tests {
         File::create(&file2)?;
         create_dir(dir2)?;
 
-        let (paths, _) = python_files_in_path(
+        let (paths, _) = project_files_in_path(
             &[root.to_path_buf()],
             &PyprojectConfig::new(PyprojectDiscoveryStrategy::Fixed, Settings::default(), None),
             &NoOpTransformer,
diff --git a/crates/ruff_workspace/src/settings.rs b/crates/ruff_workspace/src/settings.rs
index 6e3159e5266dc..98befe4b775fd 100644
--- a/crates/ruff_workspace/src/settings.rs
+++ b/crates/ruff_workspace/src/settings.rs
@@ -150,6 +150,7 @@ pub(crate) static INCLUDE_PREVIEW: &[FilePattern] = &[
     FilePattern::Builtin("*.pyw"),
     FilePattern::Builtin("*.ipynb"),
     FilePattern::Builtin("**/pyproject.toml"),
+    FilePattern::Builtin("*.md"),
 ];
 
 impl FileResolverSettings {
diff --git a/docs/formatter.md b/docs/formatter.md
index ebf09308aa5ad..4bd968d7f1c3b 100644
--- a/docs/formatter.md
+++ b/docs/formatter.md
@@ -285,43 +285,6 @@ to `<!-- fmt:off -->` and `<!-- fmt:on -->` respectively.
 
 [blacken-docs]: https://github.com/adamchainz/blacken-docs/
 
-Ruff will not automatically discover or format Markdown files in your project,
-but will format any Markdown files explicitly passed with a `.md` extension:
-
-```shell-session
-$ ruff format --preview --check docs/
-warning: No Python files found under the given path(s)
-
-$ ruff format --preview --check docs/*.md
-13 files already formatted
-```
-
-This is likely to change in a future release when the feature is stabilized.
-Including Markdown files without also enabling [preview mode](preview.md#preview)
-will result in an error message and non-zero [exit code](#exit-codes).
-
-To include Markdown files by default when running Ruff on your project, add them
-with [`extend-include`](settings.md#extend-include) in your project settings:
-
-=== "pyproject.toml"
-
-    ```toml
-    [tool.ruff]
-    # Find and format code blocks in Markdown files
-    extend-include = ["*.md"]
-    # OR
-    extend-include = ["docs/*.md"]
-    ```
-
-=== "ruff.toml"
-
-    ```toml
-    # Find and format code blocks in Markdown files
-    extend-include = ["*.md"]
-    # OR
-    extend-include = ["docs/*.md"]
-    ```
-
 To format Markdown files with extensions other than `.md`, configure custom
 [`extension`](settings.md#extension) mappings. Ruff will automatically include
 these mapped extensions in file discovery:
@@ -353,6 +316,24 @@ repos:
         types_or: [python, pyi, jupyter, markdown]
 ```
 
+To *disable* formatting of Markdown files, add them to
+[`extend-exclude`](settings.md#extend-exclude) in your project settings:
+
+=== "pyproject.toml"
+
+    ```toml
+    [tool.ruff]
+    # Disable formatting in Markdown files
+    extend-exclude = ["*.md"]
+    ```
+
+=== "ruff.toml"
+
+    ```toml
+    # Disable formatting in Markdown files
+    extend-exclude = ["*.md"]
+    ```
+
 ## Format suppression
 
 Like Black, Ruff supports `# fmt: on`, `# fmt: off`, and `# fmt: skip` pragma comments, which can