diff --git a/qlty-cli/src/commands/init.rs b/qlty-cli/src/commands/init.rs
index 0ed7e2c7d..67045f379 100644
--- a/qlty-cli/src/commands/init.rs
+++ b/qlty-cli/src/commands/init.rs
@@ -41,13 +41,21 @@ pub struct Init {
     #[arg(long, value_parser = SourceSpec::new)]
     pub source: Option<SourceSpec>,
 
+    /// Warning: this option has been deprecated!
     /// Enable plugin prefix detection.
-    #[arg(long)]
+    #[arg(hide = true, long)]
     pub with_prefixes: bool,
 }
 
 impl Init {
     pub fn execute(&self, args: &Arguments) -> Result<CommandSuccess, CommandError> {
+        if self.with_prefixes {
+            eprintln!(
+                "{} The --with-prefixes option has been deprecated and is no longer needed.",
+                style("⚠").yellow()
+            );
+        }
+
         if !args.no_upgrade_check {
             QltyRelease::upgrade_check().ok();
         }
@@ -77,7 +85,6 @@ impl Init {
                 skip_plugins: self.skip_plugins,
                 skip_default_source: self.skip_default_source,
                 source: self.source.clone(),
-                with_prefixes: self.with_prefixes,
             })?;
 
             initializer.prepare()?;
diff --git a/qlty-cli/src/initializer/scanner.rs b/qlty-cli/src/initializer/scanner.rs
index b24d0f4ab..1e3142ca2 100644
--- a/qlty-cli/src/initializer/scanner.rs
+++ b/qlty-cli/src/initializer/scanner.rs
@@ -128,7 +128,6 @@ impl Scanner {
                         package_filters,
                         plugin_initializer,
                         path_osstr,
-                        self.settings.with_prefixes,
                     );
                 }
 
@@ -355,7 +354,6 @@ impl Scanner {
         package_filters: Vec<String>,
         plugin_initializer: &PluginInitializer,
         path: &str,
-        with_prefixes: bool,
     ) {
         if let Some(plugin_to_activate) =
             plugins_to_activate.get_mut(&plugin_initializer.plugin_name)
@@ -365,21 +363,12 @@ impl Scanner {
                 .extend(package_filters.clone());
 
             if let Some(package_file) = &plugin_to_activate.package_file {
-                if with_prefixes {
-                    plugin_to_activate.package_file = Self::process_plugin_package_file_prefix(
-                        package_file,
-                        &mut plugin_to_activate.prefixes,
-                    );
+                plugin_to_activate.package_file = Self::process_plugin_package_file_prefix(
+                    package_file,
+                    &mut plugin_to_activate.prefixes,
+                );
 
-                    Self::process_plugin_package_file_prefix(
-                        path,
-                        &mut plugin_to_activate.prefixes,
-                    );
-                } else if PathBuf::from(path).components().count()
-                    < PathBuf::from(package_file).components().count()
-                {
-                    plugin_to_activate.package_file = Some(path.to_owned());
-                }
+                Self::process_plugin_package_file_prefix(path, &mut plugin_to_activate.prefixes);
             } else {
                 plugin_to_activate.package_file = Some(path.to_owned());
             }
@@ -501,7 +490,6 @@ config_files = ["config.toml"]
             skip_plugins: false,
             skip_default_source: true,
             source: Some(source_spec.clone()),
-            with_prefixes: false,
         };
 
         (
@@ -628,62 +616,6 @@ config_files = ["config.toml"]
             .is_none());
     }
 
-    #[test]
-    fn test_insert_package_filters_and_package_file_simple() {
-        let mut plugins_to_activate = HashMap::new();
-        let plugin_initializer = PluginInitializer {
-            plugin_name: "test".to_string(),
-            package_file_candidate: None,
-            package_file_candidate_filters: vec![],
-            driver_initializers: vec![],
-        };
-
-        let path = "deep/package.json";
-
-        Scanner::insert_package_filters_and_package_file(
-            &mut plugins_to_activate,
-            vec!["test".to_string()],
-            &plugin_initializer,
-            path,
-            false,
-        );
-
-        assert_eq!(plugins_to_activate.len(), 1);
-        assert_eq!(
-            plugins_to_activate.get("test").unwrap().package_file,
-            Some(path.to_string())
-        );
-        assert_eq!(
-            plugins_to_activate.get("test").unwrap().package_filters,
-            vec!["test".to_string()]
-        );
-
-        let path = "package.json";
-
-        Scanner::insert_package_filters_and_package_file(
-            &mut plugins_to_activate,
-            vec!["test2".to_string()],
-            &plugin_initializer,
-            path,
-            false,
-        );
-
-        assert_eq!(plugins_to_activate.len(), 1);
-        assert_eq!(
-            plugins_to_activate.get("test").unwrap().package_file,
-            Some(path.to_string())
-        );
-        assert_eq!(
-            plugins_to_activate.get("test").unwrap().package_filters,
-            vec!["test".to_string(), "test2".to_string()]
-        );
-
-        assert_eq!(
-            plugins_to_activate.get("test").unwrap().prefixes,
-            HashSet::new()
-        );
-    }
-
     #[test]
     fn test_insert_package_filters_and_package_file_with_prefixes() {
         let mut plugins_to_activate = HashMap::new();
@@ -701,7 +633,6 @@ config_files = ["config.toml"]
             vec!["test".to_string()],
             &plugin_initializer,
             path,
-            false,
         );
 
         assert_eq!(plugins_to_activate.len(), 1);
@@ -726,7 +657,6 @@ config_files = ["config.toml"]
             vec!["test2".to_string()],
             &plugin_initializer,
             path,
-            true,
         );
 
         assert_eq!(plugins_to_activate.len(), 1);
diff --git a/qlty-cli/src/initializer/settings.rs b/qlty-cli/src/initializer/settings.rs
index 52570f1d2..b7ae44de8 100644
--- a/qlty-cli/src/initializer/settings.rs
+++ b/qlty-cli/src/initializer/settings.rs
@@ -7,5 +7,4 @@ pub struct Settings {
     pub skip_plugins: bool,
     pub skip_default_source: bool,
     pub source: Option<SourceSpec>,
-    pub with_prefixes: bool,
 }
diff --git a/qlty-cli/tests/cmd/init/prefix.toml b/qlty-cli/tests/cmd/init/prefix.toml
index d9faa3e55..9a7b8c9ae 100644
--- a/qlty-cli/tests/cmd/init/prefix.toml
+++ b/qlty-cli/tests/cmd/init/prefix.toml
@@ -1,2 +1,2 @@
 bin.name = "qlty"
-args = ["init", "--dry-run", "--skip-default-source", "--source", "local=../plugins", "--no-upgrade-check", "--with-prefixes"]
+args = ["init", "--dry-run", "--skip-default-source", "--source", "local=../plugins", "--no-upgrade-check"]