diff --git a/lib/cli/src/commands/run/mod.rs b/lib/cli/src/commands/run/mod.rs
index d91a3ed4296..4abed422fbd 100644
--- a/lib/cli/src/commands/run/mod.rs
+++ b/lib/cli/src/commands/run/mod.rs
@@ -423,7 +423,8 @@ impl Run {
         uses: Vec<BinaryPackage>,
         runtime: Arc<dyn Runtime + Send + Sync>,
     ) -> Result<(), Error> {
-        let mut runner = self.build_wasi_runner(&runtime)?;
+        // Assume webcs are always WASIX
+        let mut runner = self.build_wasi_runner(&runtime, true)?;
         Runner::run_command(&mut runner, command_name, pkg, runtime)
     }
 
@@ -506,7 +507,7 @@ impl Run {
         pkg: &BinaryPackage,
         runtime: Arc<dyn Runtime + Send + Sync>,
     ) -> Result<(), Error> {
-        let mut inner = self.build_wasi_runner(&runtime)?;
+        let mut inner = self.build_wasi_runner(&runtime, true)?;
         let mut runner = wasmer_wasix::runners::dproxy::DProxyRunner::new(inner, pkg);
         runner.run_command(command_name, pkg, runtime)
     }
@@ -555,12 +556,13 @@ impl Run {
     fn build_wasi_runner(
         &self,
         runtime: &Arc<dyn Runtime + Send + Sync>,
+        is_wasix: bool,
     ) -> Result<WasiRunner, anyhow::Error> {
         let packages = self.load_injected_packages(runtime)?;
 
         let mut runner = WasiRunner::new();
 
-        let (is_home_mapped, mapped_diretories) = self.wasi.build_mapped_directories()?;
+        let (is_home_mapped, mapped_diretories) = self.wasi.build_mapped_directories(is_wasix)?;
 
         runner
             .with_args(&self.args)
@@ -625,7 +627,7 @@ impl Run {
     ) -> Result<(), Error> {
         let program_name = wasm_path.display().to_string();
 
-        let runner = self.build_wasi_runner(&runtime)?;
+        let runner = self.build_wasi_runner(&runtime, wasmer_wasix::is_wasix_module(&module))?;
         runner.run_wasm(
             RuntimeOrEngine::Runtime(runtime),
             &program_name,
diff --git a/lib/cli/src/commands/run/wasi.rs b/lib/cli/src/commands/run/wasi.rs
index e324e668e26..33336136d38 100644
--- a/lib/cli/src/commands/run/wasi.rs
+++ b/lib/cli/src/commands/run/wasi.rs
@@ -495,7 +495,10 @@ impl Wasi {
         Ok(Vec::new())
     }
 
-    pub fn build_mapped_directories(&self) -> Result<(bool, Vec<MappedDirectory>), anyhow::Error> {
+    pub fn build_mapped_directories(
+        &self,
+        is_wasix: bool,
+    ) -> Result<(bool, Vec<MappedDirectory>), anyhow::Error> {
         let mut mapped_dirs = Vec::new();
 
         // Process the --dirs flag and merge it with --mapdir.
@@ -514,9 +517,19 @@ impl Wasi {
 
                 MappedDirectory {
                     host: current_dir,
-                    guest: MAPPED_CURRENT_DIR_DEFAULT_PATH.to_string(),
+                    guest: if is_wasix {
+                        MAPPED_CURRENT_DIR_DEFAULT_PATH.to_string()
+                    } else {
+                        "/".to_string()
+                    },
                 }
             } else {
+                if dir == Path::new("/") && is_wasix {
+                    tracing::warn!(
+                        "Pre-opening the root directory with --dir=/ breaks WASIX modules' filesystems"
+                    );
+                }
+
                 let resolved = dir.canonicalize().with_context(|| {
                     format!(
                         "could not canonicalize path for argument '--dir {}'",
@@ -551,11 +564,18 @@ impl Wasi {
         }
 
         for MappedDirectory { host, guest } in &self.mapped_dirs {
+            if guest == "/" && is_wasix {
+                // Note: it appears we canonicalize the path before this point and showing the value of
+                // `host` in the error message may throw users off, so we use a placeholder.
+                tracing::warn!(
+                    "Mounting on the guest's virtual root with --mapdir /:<HOST_PATH> breaks WASIX modules' filesystems"
+                );
+            }
             let resolved_host = host.canonicalize().with_context(|| {
                 format!(
                     "could not canonicalize path for argument '--mapdir {}:{}'",
-                    host.display(),
                     guest,
+                    host.display(),
                 )
             })?;
 
@@ -569,7 +589,11 @@ impl Wasi {
 
                 MappedDirectory {
                     host: resolved_host,
-                    guest: MAPPED_CURRENT_DIR_DEFAULT_PATH.to_string(),
+                    guest: if is_wasix {
+                        MAPPED_CURRENT_DIR_DEFAULT_PATH.to_string()
+                    } else {
+                        "/".to_string()
+                    },
                 }
             } else {
                 MappedDirectory {
diff --git a/lib/wasix/src/runtime/package_loader/load_package_tree.rs b/lib/wasix/src/runtime/package_loader/load_package_tree.rs
index d8f5dd4ed62..d679a5ff38f 100644
--- a/lib/wasix/src/runtime/package_loader/load_package_tree.rs
+++ b/lib/wasix/src/runtime/package_loader/load_package_tree.rs
@@ -466,9 +466,6 @@ fn filesystem_v3(
 ) -> Result<UnionFileSystem, Error> {
     let mut volumes: HashMap<&PackageId, BTreeMap<String, Volume>> = HashMap::new();
 
-    let mut mountings: Vec<_> = pkg.filesystem.iter().collect();
-    mountings.sort_by_key(|m| std::cmp::Reverse(m.mount_path.as_path()));
-
     let union_fs = UnionFileSystem::new();
 
     for ResolvedFileSystemMapping {
@@ -482,6 +479,12 @@ fn filesystem_v3(
             continue;
         }
 
+        if mount_path.as_path() == Path::new("/") {
+            tracing::warn!(
+                "The \"{package}\" package wants to mount a volume at \"/\", which breaks WASIX modules' filesystems",
+            );
+        }
+
         // Note: We want to reuse existing Volume instances if we can. That way
         // we can keep the memory usage down. A webc::compat::Volume is
         // reference-counted, anyway.
@@ -538,9 +541,6 @@ fn filesystem_v2(
 ) -> Result<UnionFileSystem, Error> {
     let mut volumes: HashMap<&PackageId, BTreeMap<String, Volume>> = HashMap::new();
 
-    let mut mountings: Vec<_> = pkg.filesystem.iter().collect();
-    mountings.sort_by_key(|m| std::cmp::Reverse(m.mount_path.as_path()));
-
     let union_fs = UnionFileSystem::new();
 
     for ResolvedFileSystemMapping {
@@ -554,6 +554,12 @@ fn filesystem_v2(
             continue;
         }
 
+        if mount_path.as_path() == Path::new("/") {
+            tracing::warn!(
+                "The \"{package}\" package wants to mount a volume at \"/\", which breaks WASIX modules' filesystems",
+            );
+        }
+
         // Note: We want to reuse existing Volume instances if we can. That way
         // we can keep the memory usage down. A webc::compat::Volume is
         // reference-counted, anyway.