diff --git a/crates/turborepo-lib/src/cli.rs b/crates/turborepo-lib/src/cli.rs
index 7c2a460f133ed..82be20ce08861 100644
--- a/crates/turborepo-lib/src/cli.rs
+++ b/crates/turborepo-lib/src/cli.rs
@@ -4,6 +4,7 @@ use anyhow::{anyhow, Result};
 use camino::Utf8PathBuf;
 use clap::{ArgAction, CommandFactory, Parser, Subcommand, ValueEnum};
 use clap_complete::{generate, Shell};
+use itertools::Itertools;
 use serde::{Deserialize, Serialize};
 use tracing::{debug, error};
 use turbopath::AbsoluteSystemPathBuf;
@@ -202,8 +203,42 @@ pub enum LinkTarget {
 
 impl Args {
     pub fn new() -> Result<Self> {
-        let mut clap_args = match Args::try_parse() {
-            Ok(args) => args,
+        // We always pass --single-package in from the shim.
+        // We need to omit it, and then add it in for run.
+        let arg_separator_position =
+            std::env::args_os().position(|input_token| input_token == "--");
+
+        let single_package_position =
+            std::env::args_os().position(|input_token| input_token == "--single-package");
+
+        let is_single_package = match (arg_separator_position, single_package_position) {
+            (_, None) => false,
+            (None, Some(_)) => true,
+            (Some(arg_separator_position), Some(single_package_position)) => {
+                single_package_position < arg_separator_position
+            }
+        };
+
+        // Clap supports arbitrary iterators as input.
+        // We can remove all instances of --single-package
+        let single_package_free = std::env::args_os()
+            .enumerate()
+            .filter(|(index, input_token)| {
+                arg_separator_position
+                    .is_some_and(|arg_separator_position| index > &arg_separator_position)
+                    || input_token != "--single-package"
+            })
+            .map(|(_, input_token)| input_token);
+
+        let mut clap_args = match Args::try_parse_from(single_package_free) {
+            Ok(mut args) => {
+                // And then only add them back in when we're in `run`.
+                if let Some(ref mut run_args) = args.run_args {
+                    run_args.single_package = is_single_package
+                }
+
+                args
+            }
             // Don't use error logger when displaying help text
             Err(e)
                 if matches!(