diff --git a/Cargo.lock b/Cargo.lock
index e7a1874e46..df6196d22f 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -1444,7 +1444,7 @@ dependencies = [
 [[package]]
 name = "deno_config"
 version = "0.39.3"
-source = "git+https://github.com/denoland/deno_config.git?rev=81d8e844624a8f6b3961213d1480dcc923d08b11#81d8e844624a8f6b3961213d1480dcc923d08b11"
+source = "git+https://github.com/denoland/deno_config.git?rev=0d588fb1831bf4d33d3279a1a75db6138d81a75b#0d588fb1831bf4d33d3279a1a75db6138d81a75b"
 dependencies = [
  "anyhow",
  "deno_package_json",
diff --git a/Cargo.toml b/Cargo.toml
index 80b1ab3de4..fc379cee73 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -52,7 +52,7 @@ deno_core = { version = "0.324.0" }
 
 deno_bench_util = { version = "0.175.0", path = "./bench_util" }
 # TODO(nayeemrmn): Use proper version when https://github.com/denoland/deno_config/pull/143 lands!
-deno_config = { git = "https://github.com/denoland/deno_config.git", rev = "81d8e844624a8f6b3961213d1480dcc923d08b11", features = ["workspace", "sync"] }
+deno_config = { git = "https://github.com/denoland/deno_config.git", rev = "0d588fb1831bf4d33d3279a1a75db6138d81a75b", features = ["workspace", "sync"] }
 deno_lockfile = "=0.23.2"
 deno_media_type = { version = "0.2.0", features = ["module_specifier"] }
 deno_npm = "=0.26.0"
diff --git a/cli/tools/check.rs b/cli/tools/check.rs
index 53b89f21b7..bc6fe0d44b 100644
--- a/cli/tools/check.rs
+++ b/cli/tools/check.rs
@@ -9,8 +9,6 @@ use std::sync::Arc;
 
 use deno_ast::MediaType;
 use deno_ast::ModuleSpecifier;
-use deno_config::glob::FilePatterns;
-use deno_config::glob::PathOrPattern;
 use deno_core::error::AnyError;
 use deno_core::futures::FutureExt;
 use deno_graph::Module;
@@ -59,45 +57,14 @@ pub async fn check(
   if is_discovered_config {
     let factory = CliFactory::from_flags(flags.clone());
     let cli_options = factory.cli_options()?;
-    let (remote_files, files) = check_flags
-      .files
-      .iter()
-      .cloned()
-      .partition::<Vec<_>, _>(|f| {
-        f.starts_with("http://")
-          || f.starts_with("https://")
-          || f.starts_with("npm:")
-          || f.starts_with("jsr:")
-      });
-    let mut by_workspace_directory = cli_options
+    let by_workspace_directory = cli_options
       .resolve_file_flags_for_members(&FileFlags {
         ignore: Default::default(),
-        include: files,
+        include: check_flags.files,
       })?
       .into_iter()
       .map(|(d, p)| (d.dir_url().clone(), (Arc::new(d), p)))
       .collect::<BTreeMap<_, _>>();
-    if !remote_files.is_empty() {
-      by_workspace_directory
-        .entry(cli_options.start_dir.dir_url().clone())
-        .or_insert((
-          cli_options.start_dir.clone(),
-          FilePatterns {
-            base: cli_options.initial_cwd().to_path_buf(),
-            include: Some(Default::default()),
-            exclude: Default::default(),
-          },
-        ))
-        .1
-        .include
-        .get_or_insert_with(Default::default)
-        .append(
-          remote_files
-            .iter()
-            .flat_map(|s| ModuleSpecifier::parse(s).ok())
-            .map(PathOrPattern::RemoteUrl),
-        );
-    }
     let container = WorkspaceFileContainer::from_workspace_dirs_with_files(
       by_workspace_directory.into_values().collect(),
       |patterns, cli_options, _| {