diff --git a/crates/ruff_dev/src/check_formatter_stability.rs b/crates/ruff_dev/src/check_formatter_stability.rs
index 26b1d68902e4d6..39f90224b20208 100644
--- a/crates/ruff_dev/src/check_formatter_stability.rs
+++ b/crates/ruff_dev/src/check_formatter_stability.rs
@@ -42,6 +42,9 @@ pub(crate) struct Args {
     /// Print only the first error and exit, `-x` is same as pytest
     #[arg(long, short = 'x')]
     pub(crate) exit_first_error: bool,
+    /// Checks each project inside a directory
+    #[arg(long)]
+    pub(crate) multi_project: bool,
 }
 
 /// Generate ourself a `try_parse_from` impl for `CheckArgs`. This is a strange way to use clap but
@@ -54,6 +57,35 @@ struct WrapperArgs {
 }
 
 pub(crate) fn main(args: &Args) -> anyhow::Result<ExitCode> {
+    let all_success = if args.multi_project {
+        let mut all_success = true;
+        for base_dir in &args.files {
+            for dir in base_dir.read_dir()? {
+                let dir = dir?;
+                println!("Starting {}", dir.path().display());
+                let success = check_repo(&Args {
+                    files: vec![dir.path().clone()],
+                    ..*args
+                });
+                println!("Finished {}: {:?}", dir.path().display(), success);
+                if !matches!(success, Ok(true)) {
+                    all_success = false;
+                }
+            }
+        }
+        all_success
+    } else {
+        check_repo(args)?
+    };
+    if all_success {
+        Ok(ExitCode::SUCCESS)
+    } else {
+        Ok(ExitCode::FAILURE)
+    }
+}
+
+/// Returns whether the check was successful
+pub(crate) fn check_repo(args: &Args) -> anyhow::Result<bool> {
     let start = Instant::now();
 
     // Find files to check (or in this case, format twice). Adapted from ruff_cli
@@ -77,13 +109,20 @@ pub(crate) fn main(args: &Args) -> anyhow::Result<ExitCode> {
     let (paths, _resolver) = python_files_in_path(&cli.files, &pyproject_config, &overrides)?;
     assert!(!paths.is_empty(), "no python files in {:?}", cli.files);
 
+    let mut formatted_counter = 0;
     let errors = paths
         .into_iter()
         .map(|dir_entry| {
             // Doesn't make sense to recover here in this test script
-            let file = dir_entry
-                .expect("Iterating the files in the repository failed")
-                .into_path();
+            dir_entry.expect("Iterating the files in the repository failed")
+        })
+        .filter(|dir_entry| {
+            // For some reason it does not filter in the beginning
+            dir_entry.file_name() != "pyproject.toml"
+        })
+        .map(|dir_entry| {
+            let file = dir_entry.path().to_path_buf();
+            formatted_counter += 1;
             // Handle panics (mostly in `debug_assert!`)
             let result = match catch_unwind(|| check_file(&file)) {
                 Ok(result) => result,
@@ -166,20 +205,20 @@ Formatted twice:
         }
 
         if args.exit_first_error {
-            return Ok(ExitCode::FAILURE);
+            return Ok(false);
         }
     }
     let duration = start.elapsed();
     println!(
         "Formatting {} files twice took {:.2}s",
-        cli.files.len(),
+        formatted_counter,
         duration.as_secs_f32()
     );
 
     if any_errors {
-        Ok(ExitCode::FAILURE)
+        Ok(false)
     } else {
-        Ok(ExitCode::SUCCESS)
+        Ok(true)
     }
 }
 
diff --git a/scripts/check_ecosystem.py b/scripts/check_ecosystem.py
index d60ad3fc6dd061..c8c19162999c08 100755
--- a/scripts/check_ecosystem.py
+++ b/scripts/check_ecosystem.py
@@ -44,11 +44,11 @@ class Repository(NamedTuple):
     async def clone(self: Self, checkout_dir: Path) -> AsyncIterator[Path]:
         """Shallow clone this repository to a temporary directory."""
         if checkout_dir.exists():
-            logger.debug(f"Reusing {self.org}/{self.repo}")
+            logger.debug(f"Reusing {self.org}:{self.repo}")
             yield Path(checkout_dir)
             return
 
-        logger.debug(f"Cloning {self.org}/{self.repo}")
+        logger.debug(f"Cloning {self.org}:{self.repo}")
         git_command = [
             "git",
             "clone",
@@ -177,18 +177,17 @@ async def compare(
     """Check a specific repository against two versions of ruff."""
     removed, added = set(), set()
 
-    # Allows to keep the checkouts locations
+    # By the default, the git clone are transient, but if the user provides a
+    # directory for permanent storage we keep it there
     if checkouts:
-        checkout_parent = checkouts.joinpath(repo.org)
-        # Don't create the repodir itself, we need that for checking for existing
-        # clones
-        checkout_parent.mkdir(exist_ok=True, parents=True)
-        location_context = nullcontext(checkout_parent)
+        location_context = nullcontext(checkouts)
     else:
         location_context = tempfile.TemporaryDirectory()
 
     with location_context as checkout_parent:
-        checkout_dir = Path(checkout_parent).joinpath(repo.repo)
+        assert ":" not in repo.org
+        assert ":" not in repo.repo
+        checkout_dir = Path(checkout_parent).joinpath(f"{repo.org}:{repo.repo}")
         async with repo.clone(checkout_dir) as path:
             try:
                 async with asyncio.TaskGroup() as tg:
@@ -284,8 +283,19 @@ async def main(
 
     logger.debug(f"Checking {len(repositories)} projects")
 
+    # https://stackoverflow.com/a/61478547/3549270
+    # Otherwise doing 3k repositories can take >8GB RAM
+    semaphore = asyncio.Semaphore(50)
+
+    async def limited_parallelism(coroutine):  # noqa: ANN
+        async with semaphore:
+            return await coroutine
+
     results = await asyncio.gather(
-        *[compare(ruff1, ruff2, repo, checkouts) for repo in repositories.values()],
+        *[
+            limited_parallelism(compare(ruff1, ruff2, repo, checkouts))
+            for repo in repositories.values()
+        ],
         return_exceptions=True,
     )
 
@@ -433,6 +443,8 @@ async def main(
         logging.basicConfig(level=logging.INFO)
 
     loop = asyncio.get_event_loop()
+    if args.checkouts:
+        args.checkouts.mkdir(exist_ok=True, parents=True)
     main_task = asyncio.ensure_future(
         main(
             ruff1=args.ruff1,