diff --git a/src/scikit_build_core/_compat/importlib/resources.py b/src/scikit_build_core/_compat/importlib/resources.py
index dba901f9..2e5c96d2 100644
--- a/src/scikit_build_core/_compat/importlib/resources.py
+++ b/src/scikit_build_core/_compat/importlib/resources.py
@@ -7,7 +7,17 @@
 else:
     from importlib.resources import files
 
-__all__ = ["files"]
+if sys.version_info < (3, 10):
+    # Readers were introduced in 3.10
+    from importlib_resources import readers
+elif sys.version_info < (3, 11):
+    # In 3.10 readers were implemented in importlib.readers
+    from importlib import readers
+else:
+    # From 3.11 it is accessed as importlib.resources.readers
+    from importlib.resources import readers
+
+__all__ = ["files", "readers"]
 
 
 def __dir__() -> list[str]:
diff --git a/src/scikit_build_core/builder/builder.py b/src/scikit_build_core/builder/builder.py
index 8492c469..d44cb835 100644
--- a/src/scikit_build_core/builder/builder.py
+++ b/src/scikit_build_core/builder/builder.py
@@ -23,6 +23,7 @@
 
 if TYPE_CHECKING:
     from collections.abc import Generator, Iterable, Mapping, Sequence
+    from typing import Any
 
     from packaging.version import Version
 
@@ -84,6 +85,68 @@ def _filter_env_cmake_args(env_cmake_args: list[str]) -> Generator[str, None, No
             yield arg
 
 
+# Type-hinting for Traversable is rather hard because they were introduced in python 3.11.
+# This avoids introducing importlib_resources dependency that may not be used in the actual package loader
+def _sanitize_path(path: Any) -> list[Path] | None:
+    if isinstance(path, resources.readers.MultiplexedPath):
+        # pylint: disable-next=protected-access
+        return path._paths
+    if isinstance(path, Path):
+        return [path]
+    logger.warning("Unknown path type: [{}] {}", type(path), path)
+    return None
+
+
+def _handle_search_paths(
+    entry_point: str,
+    settings_val: list[str] | dict[str, str] | None,
+    output: list[Path] | dict[str, list[Path]],
+) -> None:
+    # Sanity checks
+    if isinstance(output, dict):
+        assert isinstance(settings_val, dict)
+
+    # Get the search paths from the entry points
+    search_paths_dict = {}
+    eps = metadata.entry_points(group=entry_point)
+    if eps:
+        logger.debug(
+            "Loading search paths {} from entry-points: {}", entry_point, len(eps)
+        )
+        for ep in eps:
+            ep_value = _sanitize_path(resources.files(ep.load()))
+            logger.debug("{}: {} -> {}", ep.name, ep.value, ep_value)
+            if ep_value:
+                search_paths_dict[ep.name] = ep_value
+
+    # Update the search paths from the settings options
+    if isinstance(settings_val, dict) and settings_val:
+        logger.debug(
+            "Overriding search paths {} from config: {}", entry_point, settings_val
+        )
+        for key, val in settings_val.items():
+            if val:
+                # TODO: Allow settings_val to be dict[str, list[str]]?
+                search_paths_dict[key] = [Path(val)]
+            else:
+                search_paths_dict.pop(key)
+
+    # Write to the output
+    if isinstance(output, list):
+        search_paths_list = [
+            path for ep_values in search_paths_dict.values() for path in ep_values
+        ]
+        # If the settings options was a list the values are appended as-is
+        if isinstance(settings_val, list) and settings_val:
+            logger.debug(
+                "Appending search paths {} with config: {}", entry_point, settings_val
+            )
+            search_paths_list += map(Path, settings_val)
+        output.extend(search_paths_list)
+        return
+    output.update(search_paths_dict)
+
+
 @dataclasses.dataclass
 class Builder:
     settings: ScikitBuildSettings
@@ -123,47 +186,20 @@ def configure(
         }
 
         # Add any extra CMake modules
-        module_dirs_dict = {
-            ep.name: resources.files(ep.load())
-            for ep in metadata.entry_points(group="cmake.module")
-        }
-        if isinstance(self.settings.search.modules, dict):
-            # Allow to override any entry-point definition
-            module_dirs_dict.update(self.settings.search.modules)
-        module_dirs = list(module_dirs_dict.values())
-        if isinstance(self.settings.search.modules, list):
-            # If it was a list, append to the entry-point definitions
-            module_dirs += self.settings.search.modules
-        # Remove any empty paths
-        module_dirs = [path for path in module_dirs if path]
-        self.config.module_dirs.extend(module_dirs)
+        _handle_search_paths(
+            "cmake.module", self.settings.search.modules, self.config.module_dirs
+        )
 
         # Add any extra CMake prefixes
-        prefix_dirs_dict = {
-            ep.name: resources.files(ep.load())
-            for ep in metadata.entry_points(group="cmake.prefix")
-        }
-        if isinstance(self.settings.search.prefixes, dict):
-            # Allow to override any entry-point definition
-            prefix_dirs_dict.update(self.settings.search.prefixes)
-        prefix_dirs = list(prefix_dirs_dict.values())
-        if isinstance(self.settings.search.prefixes, list):
-            # If it was a list, append to the entry-point definitions
-            prefix_dirs += self.settings.search.prefixes
-        # Remove any empty paths
-        prefix_dirs = [path for path in prefix_dirs if path]
-        self.config.prefix_dirs.extend(prefix_dirs)
+        _handle_search_paths(
+            "cmake.prefix", self.settings.search.prefixes, self.config.prefix_dirs
+        )
 
         # Add all CMake roots
-        prefix_roots = {
-            ep.name: resources.files(ep.load())
-            for ep in metadata.entry_points(group="cmake.root")
-        }
         # TODO: Check for unique uppercase names
-        prefix_roots.update(self.settings.search.roots)
-        # Remove any empty paths
-        prefix_roots = {pkg: path for pkg, path in prefix_roots.items() if path}
-        self.config.prefix_roots.update(prefix_roots)
+        _handle_search_paths(
+            "cmake.root", self.settings.search.roots, self.config.prefix_roots
+        )
 
         # Add site-packages to the prefix path for CMake
         site_packages = Path(sysconfig.get_path("purelib"))
diff --git a/src/scikit_build_core/cmake.py b/src/scikit_build_core/cmake.py
index 403e5f12..5a14b52c 100644
--- a/src/scikit_build_core/cmake.py
+++ b/src/scikit_build_core/cmake.py
@@ -79,7 +79,7 @@ class CMaker:
     build_type: str
     module_dirs: list[Path] = dataclasses.field(default_factory=list)
     prefix_dirs: list[Path] = dataclasses.field(default_factory=list)
-    prefix_roots: dict[str, Path] = dataclasses.field(default_factory=dict)
+    prefix_roots: dict[str, list[Path]] = dataclasses.field(default_factory=dict)
     init_cache_file: Path = dataclasses.field(init=False, default=Path())
     env: dict[str, str] = dataclasses.field(init=False, default_factory=os.environ.copy)
     single_config: bool = not sysconfig.get_platform().startswith("win")
@@ -185,14 +185,14 @@ def init_cache(
                 f.write('set(CMAKE_FIND_ROOT_PATH_MODE_PACKAGE "BOTH" CACHE PATH "")\n')
 
             if self.prefix_roots:
-                for pkg, path in self.prefix_roots.items():
-                    path_str = str(path).replace("\\", "/")
+                for pkg, path_list in self.prefix_roots.items():
+                    paths_str = ";".join(map(str, path_list)).replace("\\", "/")
                     f.write(
-                        f'set({pkg}_ROOT [===[{path_str}]===] CACHE PATH "" FORCE)\n'
+                        f'set({pkg}_ROOT [===[{paths_str}]===] CACHE PATH "" FORCE)\n'
                     )
                     # Available since CMake 3.27 with CMP0144
                     f.write(
-                        f'set({pkg.upper()}_ROOT [===[{path_str}]===] CACHE PATH "" FORCE)\n'
+                        f'set({pkg.upper()}_ROOT [===[{paths_str}]===] CACHE PATH "" FORCE)\n'
                     )
 
         contents = self.init_cache_file.read_text(encoding="utf-8").strip()
diff --git a/src/scikit_build_core/settings/skbuild_model.py b/src/scikit_build_core/settings/skbuild_model.py
index 6b3bbba8..0f8fc39e 100644
--- a/src/scikit_build_core/settings/skbuild_model.py
+++ b/src/scikit_build_core/settings/skbuild_model.py
@@ -93,19 +93,19 @@ class SearchSettings:
     Add the wheel build path to the CMake prefix paths.
     """
 
-    modules: Optional[Union[List[Path], Dict[str, Path]]] = None
+    modules: Optional[Union[List[str], Dict[str, str]]] = None
     """
     List or dict of CMake module search paths. Dict from is used to override
     another package's entry-point definition. Populates `CMAKE_MODULE_PATH`.
     """
 
-    prefixes: Optional[Union[List[Path], Dict[str, Path]]] = None
+    prefixes: Optional[Union[List[str], Dict[str, str]]] = None
     """
     List or dict of CMake prefix search paths. Dict from is used to override
     another package's entry-point definition. Populates `CMAKE_PREFIX_PATH`.
     """
 
-    roots: Dict[str, Path] = dataclasses.field(default_factory=dict)
+    roots: Dict[str, str] = dataclasses.field(default_factory=dict)
     """
     Dict of package names and prefix paths. Populates `<Pkg>_ROOT`.
     """