diff --git a/Cargo.lock b/Cargo.lock
index 742a1f4b0..fc933c282 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -4324,6 +4324,7 @@ dependencies = [
  "flate2",
  "hex",
  "http_req",
+ "indexmap",
  "isatty",
  "libc",
  "log",
@@ -4608,11 +4609,12 @@ dependencies = [
 
 [[package]]
 name = "wasmer-toml"
-version = "0.5.0"
+version = "0.6.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "03d0f664e5dfad0339727ad2f4f8a7d982b4c120d87b800380e306c0dc038a49"
+checksum = "4232db0aff83ed6208d541ddcf1bf72730673528be8c4fe13c6369060f6e05a7"
 dependencies = [
  "anyhow",
+ "indexmap",
  "semver 1.0.14",
  "serde",
  "serde_cbor",
diff --git a/lib/cli/Cargo.toml b/lib/cli/Cargo.toml
index a1960afa9..49d4fad8a 100644
--- a/lib/cli/Cargo.toml
+++ b/lib/cli/Cargo.toml
@@ -63,7 +63,8 @@ dirs = { version = "4.0" }
 serde_json = { version = "1.0" }
 target-lexicon = { version = "0.12", features = ["std"] }
 prettytable-rs = "0.9.0"
-wasmer-toml = "0.5.0"
+wasmer-toml = "0.6.0"
+indexmap = "1.9.2"
 walkdir = "2.3.2"
 regex = "1.6.0"
 toml = "0.5.9"
diff --git a/lib/cli/src/commands/init.rs b/lib/cli/src/commands/init.rs
index 584c7764d..16ec43d89 100644
--- a/lib/cli/src/commands/init.rs
+++ b/lib/cli/src/commands/init.rs
@@ -1,6 +1,7 @@
 use anyhow::Context;
 use cargo_metadata::{CargoOpt, MetadataCommand};
 use clap::Parser;
+use indexmap::IndexMap;
 use std::collections::HashMap;
 use std::path::Path;
 use std::path::PathBuf;
@@ -204,7 +205,7 @@ impl Init {
         }
     }
 
-    fn get_filesystem_mapping(include: &[String]) -> Option<HashMap<String, PathBuf>> {
+    fn get_filesystem_mapping(include: &[String]) -> Option<IndexMap<String, PathBuf>> {
         if include.is_empty() {
             return None;
         }
diff --git a/lib/cli/src/commands/publish.rs b/lib/cli/src/commands/publish.rs
index 889a39f14..145092bc4 100644
--- a/lib/cli/src/commands/publish.rs
+++ b/lib/cli/src/commands/publish.rs
@@ -215,7 +215,7 @@ fn construct_tar_gz(
     }
 
     // bundle the package filesystem
-    let default = std::collections::HashMap::default();
+    let default = indexmap::IndexMap::default();
     for (_alias, path) in manifest.fs.as_ref().unwrap_or(&default).iter() {
         let normalized_path = normalize_path(cwd, path);
         let path_metadata = normalized_path.metadata().map_err(|_| {
diff --git a/lib/cli/src/commands/run.rs b/lib/cli/src/commands/run.rs
index 2c5fb3868..aa52c4339 100644
--- a/lib/cli/src/commands/run.rs
+++ b/lib/cli/src/commands/run.rs
@@ -8,7 +8,6 @@ use crate::suggestions::suggest_function_exports;
 use crate::warning;
 use anyhow::{anyhow, Context, Result};
 use clap::Parser;
-use std::collections::HashMap;
 use std::ops::Deref;
 use std::path::PathBuf;
 #[cfg(feature = "cache")]
@@ -124,7 +123,12 @@ impl RunWithPathBuf {
 
             #[cfg(feature = "wasi")]
             {
-                let default = HashMap::default();
+                // See https://github.com/wasmerio/wasmer/issues/3492 -
+                // we need IndexMap to have a stable ordering for the [fs] mapping,
+                // otherwise overlapping filesystem mappings might not work
+                // since we want to control the order of mounting directories from the
+                // wasmer.toml file
+                let default = indexmap::IndexMap::default();
                 let fs = manifest.fs.as_ref().unwrap_or(&default);
                 for (alias, real_dir) in fs.iter() {
                     let real_dir = self_clone.path.join(&real_dir);
diff --git a/lib/registry/Cargo.toml b/lib/registry/Cargo.toml
index a6608da9d..ce3523aec 100644
--- a/lib/registry/Cargo.toml
+++ b/lib/registry/Cargo.toml
@@ -20,7 +20,7 @@ serde_json = "1.0.85"
 url = "2.3.1"
 thiserror = "1.0.37"
 toml = "0.5.9"
-wasmer-toml = "0.5.0"
+wasmer-toml = "0.6.0"
 tar = "0.4.38"
 flate2 = "1.0.24"
 semver = "1.0.14"