diff --git a/lib/src/lints.rs b/lib/src/lints.rs
index d8497ecc..6417b660 100644
--- a/lib/src/lints.rs
+++ b/lib/src/lints.rs
@@ -15,7 +15,7 @@ use fn_error_context::context;
 /// if it does not exist error.
 #[context("Linting")]
 pub(crate) fn lint(root: &Dir) -> Result<()> {
-    let lints = [check_var_run, check_kernel, check_parse_kargs];
+    let lints = [check_var_run, check_kernel, check_parse_kargs, check_usretc];
     for lint in lints {
         lint(&root)?;
     }
@@ -32,6 +32,21 @@ fn check_var_run(root: &Dir) -> Result<()> {
     Ok(())
 }
 
+fn check_usretc(root: &Dir) -> Result<()> {
+    let etc_exists = root.symlink_metadata_optional("etc")?.is_some();
+    // For compatibility/conservatism don't bomb out if there's no /etc.
+    if !etc_exists {
+        return Ok(());
+    }
+    // But having both /etc and /usr/etc is not something we want to support.
+    if root.symlink_metadata_optional("usr/etc")?.is_some() {
+        anyhow::bail!(
+            "Found /usr/etc - this is a bootc implementation detail and not supported to use in containers"
+        );
+    }
+    Ok(())
+}
+
 /// Validate that we can parse the /usr/lib/bootc/kargs.d files.
 fn check_parse_kargs(root: &Dir) -> Result<()> {
     let _args = crate::kargs::get_kargs_in_root(root, ARCH)?;
@@ -88,3 +103,17 @@ fn test_kargs() -> Result<()> {
     assert!(check_parse_kargs(root).is_err());
     Ok(())
 }
+
+#[test]
+fn test_usr_etc() -> Result<()> {
+    let root = &fixture()?;
+    // This one should pass
+    check_usretc(root).unwrap();
+    root.create_dir_all("etc")?;
+    root.create_dir_all("usr/etc")?;
+    assert!(check_usretc(root).is_err());
+    root.remove_dir_all("etc")?;
+    // Now we should pass again
+    check_usretc(root).unwrap();
+    Ok(())
+}