diff --git a/cli/args/flags.rs b/cli/args/flags.rs
index c3e2b8cfb2..2e99aab82a 100644
--- a/cli/args/flags.rs
+++ b/cli/args/flags.rs
@@ -87,9 +87,8 @@ pub struct CompletionsFlags {
 
 #[derive(Clone, Debug, Eq, PartialEq)]
 pub struct CoverageFlags {
-  pub files: Vec<PathBuf>,
+  pub files: FileFlags,
   pub output: Option<PathBuf>,
-  pub ignore: Vec<PathBuf>,
   pub include: Vec<String>,
   pub exclude: Vec<String>,
   pub lcov: bool,
@@ -2430,9 +2429,11 @@ fn coverage_parse(flags: &mut Flags, matches: &clap::ArgMatches) {
   let lcov = matches.is_present("lcov");
   let output = matches.value_of("output").map(PathBuf::from);
   flags.subcommand = DenoSubcommand::Coverage(CoverageFlags {
-    files,
+    files: FileFlags {
+      include: files,
+      ignore,
+    },
     output,
-    ignore,
     include,
     exclude,
     lcov,
@@ -6100,9 +6101,11 @@ mod tests {
       r.unwrap(),
       Flags {
         subcommand: DenoSubcommand::Coverage(CoverageFlags {
-          files: vec![PathBuf::from("foo.json")],
+          files: FileFlags {
+            include: vec![PathBuf::from("foo.json")],
+            ignore: vec![],
+          },
           output: None,
-          ignore: vec![],
           include: vec![r"^file:".to_string()],
           exclude: vec![r"test\.(js|mjs|ts|jsx|tsx)$".to_string()],
           lcov: false,
@@ -6125,8 +6128,10 @@ mod tests {
       r.unwrap(),
       Flags {
         subcommand: DenoSubcommand::Coverage(CoverageFlags {
-          files: vec![PathBuf::from("foo.json")],
-          ignore: vec![],
+          files: FileFlags {
+            include: vec![PathBuf::from("foo.json")],
+            ignore: vec![],
+          },
           include: vec![r"^file:".to_string()],
           exclude: vec![r"test\.(js|mjs|ts|jsx|tsx)$".to_string()],
           lcov: true,
diff --git a/cli/tools/coverage/mod.rs b/cli/tools/coverage/mod.rs
index 075a43feaa..cbb2bd9cc1 100644
--- a/cli/tools/coverage/mod.rs
+++ b/cli/tools/coverage/mod.rs
@@ -1,6 +1,7 @@
 // Copyright 2018-2023 the Deno authors. All rights reserved. MIT license.
 
 use crate::args::CoverageFlags;
+use crate::args::FileFlags;
 use crate::args::Flags;
 use crate::colors;
 use crate::emit::get_source_hash;
@@ -555,8 +556,7 @@ impl CoverageReporter for PrettyCoverageReporter {
 }
 
 fn collect_coverages(
-  files: Vec<PathBuf>,
-  ignore: Vec<PathBuf>,
+  files: FileFlags,
 ) -> Result<Vec<ScriptCoverage>, AnyError> {
   let mut coverages: Vec<ScriptCoverage> = Vec::new();
   let file_paths = FileCollector::new(|file_path| {
@@ -564,8 +564,8 @@ fn collect_coverages(
   })
   .ignore_git_folder()
   .ignore_node_modules()
-  .add_ignore_paths(&ignore)
-  .collect_files(&files)?;
+  .add_ignore_paths(&files.ignore)
+  .collect_files(&files.include)?;
 
   for file_path in file_paths {
     let json = fs::read_to_string(file_path.as_path())?;
@@ -609,14 +609,13 @@ pub async fn cover_files(
   flags: Flags,
   coverage_flags: CoverageFlags,
 ) -> Result<(), AnyError> {
-  if coverage_flags.files.is_empty() {
+  if coverage_flags.files.include.is_empty() {
     return Err(generic_error("No matching coverage profiles found"));
   }
 
   let ps = ProcState::build(flags).await?;
 
-  let script_coverages =
-    collect_coverages(coverage_flags.files, coverage_flags.ignore)?;
+  let script_coverages = collect_coverages(coverage_flags.files)?;
   let script_coverages = filter_coverages(
     script_coverages,
     coverage_flags.include,