diff --git a/isort/api.py b/isort/api.py
index abf8bdb1..26ab8f2b 100644
--- a/isort/api.py
+++ b/isort/api.py
@@ -327,10 +327,11 @@ def check_file(
         config_trie = config_kwargs.pop("config_trie", None)
         if config_trie:
             config_info = config_trie.search(filename)
-            if config.verbose:
+            if config_info[0] and config.verbose:
                 print(f"{config_info[0]} used for file {filename}")
 
-            file_config = Config(**config_info[1])
+            if config_info[0]:
+                file_config = Config(**config_info[1])
 
     with io.File.read(filename) as source_file:
         return check_stream(
@@ -422,10 +423,11 @@ def sort_file(
         config_trie = config_kwargs.pop("config_trie", None)
         if config_trie:
             config_info = config_trie.search(filename)
-            if config.verbose:
+            if config_info[0] and config.verbose:
                 print(f"{config_info[0]} used for file {filename}")
 
-            file_config = Config(**config_info[1])
+            if config_info[0]:
+                file_config = Config(**config_info[1])
 
     with io.File.read(filename) as source_file:
         actual_file_path = file_path or source_file.path
diff --git a/isort/main.py b/isort/main.py
index 9369ddd1..c6d649db 100644
--- a/isort/main.py
+++ b/isort/main.py
@@ -1141,6 +1141,7 @@ def main(argv: Sequence[str] | None = None, stdin: TextIOWrapper | None = None)
                         show_diff=show_diff,
                         write_to_stdout=write_to_stdout,
                         extension=ext_format,
+                        disregard_skip=not resolve_all_configs,
                         config_trie=config_trie,
                     ),
                     file_names,
@@ -1156,6 +1157,7 @@ def main(argv: Sequence[str] | None = None, stdin: TextIOWrapper | None = None)
                         show_diff=show_diff,
                         write_to_stdout=write_to_stdout,
                         extension=ext_format,
+                        disregard_skip=not resolve_all_configs,
                         config_trie=config_trie,
                     )
                     for file_name in file_names
diff --git a/isort/settings.py b/isort/settings.py
index 9c22fa5a..8dd07580 100644
--- a/isort/settings.py
+++ b/isort/settings.py
@@ -774,7 +774,7 @@ def find_all_configs(path: str) -> Trie:
     Parses and stores any config file encountered in a trie and returns the root of
     the trie
     """
-    trie_root = Trie("default", {})
+    trie_root = Trie("default", {}, root_path=path)
 
     for dirpath, _, _ in os.walk(path):
         for config_file_name in CONFIG_SOURCES:
diff --git a/isort/utils.py b/isort/utils.py
index 2c4016d0..045af400 100644
--- a/isort/utils.py
+++ b/isort/utils.py
@@ -20,8 +20,14 @@ class Trie:
     associated with each file
     """
 
-    def __init__(self, config_file: str = "", config_data: dict[str, Any] | None = None) -> None:
+    def __init__(
+        self,
+        config_file: str = "",
+        config_data: dict[str, Any] | None = None,
+        root_path: str = "",
+    ) -> None:
         self.root: TrieNode = TrieNode(config_file, config_data)
+        self.root_path: Path | None = Path(root_path).resolve() if root_path else None
 
     def insert(self, config_file: str, config_data: dict[str, Any]) -> None:
         resolved_config_path_as_tuple = Path(config_file).parent.resolve().parts
@@ -41,7 +47,14 @@ def search(self, filename: str) -> tuple[str, dict[str, Any]]:
         Returns the closest config relative to filename by doing a depth
         first search on the prefix tree.
         """
-        resolved_file_path_as_tuple = Path(filename).resolve().parts
+        resolved_file_path = Path(filename).resolve()
+        if self.root_path:
+            try:
+                resolved_file_path.relative_to(self.root_path)
+            except ValueError:
+                return ("", {})
+
+        resolved_file_path_as_tuple = resolved_file_path.parts
 
         temp = self.root
 
diff --git a/tests/unit/test_main.py b/tests/unit/test_main.py
index 79421169..1a1aa838 100644
--- a/tests/unit/test_main.py
+++ b/tests/unit/test_main.py
@@ -153,6 +153,22 @@ def test_missing_default_section(tmpdir):
         main.main([str(python_file)])
 
 
+def test_resolve_all_configs_honors_skip_for_direct_file(tmp_path, capsys):
+    config_file = tmp_path / "pyproject.toml"
+    config_file.write_text("[tool.isort]\nextend_skip = ['a.py']\n")
+    python_file = tmp_path / "a.py"
+    original_content = "import sys\nimport os\n"
+    python_file.write_text(original_content)
+
+    main.main([str(python_file), "--resolve-all-configs", "--verbose"])
+
+    out, error = capsys.readouterr()
+    assert not error
+    assert "default used for file" not in out
+    assert "Skipped 1 files" in out
+    assert python_file.read_text() == original_content
+
+
 def test_ran_against_root():
     with pytest.raises(SystemExit):
         main.main(["/"])