diff --git a/strix/interface/utils.py b/strix/interface/utils.py
index 97ec59c3..0dfb7daa 100644
--- a/strix/interface/utils.py
+++ b/strix/interface/utils.py
@@ -1163,6 +1163,7 @@ def derive_local_base_name(path_str: str) -> str:
 
 def assign_workspace_subdirs(targets_info: list[dict[str, Any]]) -> None:
     name_counts: dict[str, int] = {}
+    allocated_subdirs: set[str] = set()
 
     for target in targets_info:
         target_type = target["type"]
@@ -1182,15 +1183,17 @@ def assign_workspace_subdirs(targets_info: list[dict[str, Any]]) -> None:
 
         # Avoid colliding with a subdir already allocated to another target
         # (e.g. base names ["api-2", "api", "api"] would otherwise both map to "api-2").
+        # Track allocated subdirs separately from base-name counts so a derived
+        # suffix never poisons the count of a later target sharing that name.
         max_attempts = len(targets_info) + 1
         attempts = 0
-        while workspace_subdir in name_counts and attempts < max_attempts:
+        while workspace_subdir in allocated_subdirs and attempts < max_attempts:
             count += 1
             workspace_subdir = f"{base_name}-{count}"
             attempts += 1
 
         name_counts[base_name] = count
-        name_counts[workspace_subdir] = count
+        allocated_subdirs.add(workspace_subdir)
 
         details["workspace_subdir"] = workspace_subdir
 
diff --git a/tests/test_diff_workspace_utils.py b/tests/test_diff_workspace_utils.py
index b089e5c9..2074df14 100644
--- a/tests/test_diff_workspace_utils.py
+++ b/tests/test_diff_workspace_utils.py
@@ -33,6 +33,25 @@ def test_assign_workspace_subdirs_avoids_suffix_collision() -> None:
     assert subdirs[2] not in {"api-2", "api"}
 
 
+def test_assign_workspace_subdirs_suffix_does_not_poison_later_base() -> None:
+    # Base names ["api", "api", "api-2"]: the second "api" target allocates the
+    # subdir "api-2"; the later real "api-2" target must still get a unique,
+    # non-colliding subdir without the earlier allocation poisoning its counter.
+    targets = [
+        _local_target("/srv/api"),
+        _local_target("/other/api"),
+        _local_target("/srv/api-2"),
+    ]
+
+    assign_workspace_subdirs(targets)
+
+    subdirs = [t["details"]["workspace_subdir"] for t in targets]
+    assert len(set(subdirs)) == 3
+    assert subdirs[0] == "api"
+    assert subdirs[1] == "api-2"
+    assert subdirs[2].startswith("api-2")
+
+
 def test_classify_diff_entries_copy_is_added_not_modified() -> None:
     result = _classify_diff_entries(
         [DiffEntry(status="C", path="new.py", old_path="orig.py", similarity=100)]