diff --git a/crates/ty/Cargo.toml b/crates/ty/Cargo.toml
index 4189758bb1..3ccd55c3cc 100644
--- a/crates/ty/Cargo.toml
+++ b/crates/ty/Cargo.toml
@@ -30,6 +30,7 @@ clearscreen = { workspace = true }
 colored = { workspace = true }
 crossbeam = { workspace = true }
 ctrlc = { version = "3.4.4" }
+dunce = { workspace = true }
 indicatif = { workspace = true }
 jiff = { workspace = true }
 rayon = { workspace = true }
diff --git a/crates/ty/src/args.rs b/crates/ty/src/args.rs
index f518e028db..4d14f78486 100644
--- a/crates/ty/src/args.rs
+++ b/crates/ty/src/args.rs
@@ -2,7 +2,7 @@ use crate::logging::Verbosity;
 use crate::python_version::PythonVersion;
 use clap::error::ErrorKind;
 use clap::{ArgAction, ArgMatches, Error, Parser};
-use ruff_db::system::SystemPathBuf;
+use ruff_db::system::{SystemPath, SystemPathBuf};
 use ty_combine::Combine;
 use ty_project::metadata::options::{EnvironmentOptions, Options, SrcOptions, TerminalOptions};
 use ty_project::metadata::value::{RangedValue, RelativeGlobPattern, RelativePathBuf, ValueSource};
@@ -158,7 +158,7 @@ pub(crate) struct CheckCommand {
 }
 
 impl CheckCommand {
-    pub(crate) fn into_options(self) -> Options {
+    pub(crate) fn into_options(self, project_root: &SystemPath) -> Options {
         let rules = if self.rules.is_empty() {
             None
         } else {
@@ -177,6 +177,43 @@ impl CheckCommand {
             .no_respect_ignore_files
             .then_some(false)
             .or(self.respect_ignore_files);
+
+        // When users explicitly specify directories on the command line, adds it as "dir/**/*"
+        // to include, ensuring their subfolders and subfiles are checked regardless of
+        // `pyproject.toml` original include configuration.
+        let include = {
+            let glob_patterns: Vec<RelativeGlobPattern> = {
+                self.paths
+                    .iter()
+                    .filter_map(|path| {
+                        let path = path.as_std_path();
+                        if !path.is_dir() {
+                            return None;
+                        }
+
+                        let Ok(canonical_path) = dunce::canonicalize(path) else {
+                            return None;
+                        };
+
+                        let relative_path = canonical_path
+                            .strip_prefix(project_root.as_std_path())
+                            .ok()?;
+                        let path_str = relative_path.to_str()?;
+                        let path_str = path_str.replace('\\', "/");
+                        let normalized_path = path_str.strip_suffix('/').unwrap_or(&path_str);
+
+                        Some(RelativeGlobPattern::cli(format!("{normalized_path}/**/*")))
+                    })
+                    .collect()
+            };
+
+            if glob_patterns.is_empty() {
+                None
+            } else {
+                Some(RangedValue::cli(glob_patterns))
+            }
+        };
+
         let options = Options {
             environment: Some(EnvironmentOptions {
                 python_version: self
@@ -206,6 +243,7 @@ impl CheckCommand {
                 exclude: self.exclude.map(|excludes| {
                     RangedValue::cli(excludes.iter().map(RelativeGlobPattern::cli).collect())
                 }),
+                include,
                 ..SrcOptions::default()
             }),
             rules,
diff --git a/crates/ty/src/lib.rs b/crates/ty/src/lib.rs
index f16192bcd5..23a6727ad6 100644
--- a/crates/ty/src/lib.rs
+++ b/crates/ty/src/lib.rs
@@ -124,7 +124,8 @@ fn run_check(args: CheckCommand) -> anyhow::Result<ExitStatus> {
 
     project_metadata.apply_configuration_files(&system)?;
 
-    let project_options_overrides = ProjectOptionsOverrides::new(config_file, args.into_options());
+    let project_options_overrides =
+        ProjectOptionsOverrides::new(config_file, args.into_options(&project_path));
     project_metadata.apply_overrides(&project_options_overrides);
 
     let mut db = ProjectDatabase::new(project_metadata, system)?;