diff --git a/src/scikit_build_core/builder/builder.py b/src/scikit_build_core/builder/builder.py
index 1db847a1..8492c469 100644
--- a/src/scikit_build_core/builder/builder.py
+++ b/src/scikit_build_core/builder/builder.py
@@ -123,19 +123,47 @@ def configure(
         }
 
         # Add any extra CMake modules
-        eps = metadata.entry_points(group="cmake.module")
-        self.config.module_dirs.extend(resources.files(ep.load()) for ep in eps)
+        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)
 
         # Add any extra CMake prefixes
-        eps = metadata.entry_points(group="cmake.prefix")
-        self.config.prefix_dirs.extend(resources.files(ep.load()) for ep in eps)
+        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)
 
         # Add all CMake roots
-        eps = metadata.entry_points(group="cmake.root")
+        prefix_roots = {
+            ep.name: resources.files(ep.load())
+            for ep in metadata.entry_points(group="cmake.root")
+        }
         # TODO: Check for unique uppercase names
-        self.config.prefix_roots.update(
-            {ep.name: resources.files(ep.load()) for ep in eps}
-        )
+        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)
 
         # Add site-packages to the prefix path for CMake
         site_packages = Path(sysconfig.get_path("purelib"))
diff --git a/src/scikit_build_core/resources/scikit-build.schema.json b/src/scikit_build_core/resources/scikit-build.schema.json
index 39163e09..2eda0aa8 100644
--- a/src/scikit_build_core/resources/scikit-build.schema.json
+++ b/src/scikit_build_core/resources/scikit-build.schema.json
@@ -96,6 +96,53 @@
     "search": {
       "additionalProperties": false,
       "properties": {
+        "modules": {
+          "description": "List or dict of CMake module search paths. Dict from is used to override another package's entry-point definition. Populates `CMAKE_MODULE_PATH`.",
+          "oneOf": [
+            {
+              "type": "array",
+              "items": {
+                "type": "string"
+              }
+            },
+            {
+              "type": "object",
+              "patternProperties": {
+                ".+": {
+                  "type": "string"
+                }
+              }
+            }
+          ]
+        },
+        "prefixes": {
+          "description": "List or dict of CMake prefix search paths. Dict from is used to override another package's entry-point definition. Populates `CMAKE_PREFIX_PATH`.",
+          "oneOf": [
+            {
+              "type": "array",
+              "items": {
+                "type": "string"
+              }
+            },
+            {
+              "type": "object",
+              "patternProperties": {
+                ".+": {
+                  "type": "string"
+                }
+              }
+            }
+          ]
+        },
+        "roots": {
+          "description": "Dict of package names and prefix paths. Populates `<Pkg>_ROOT`.",
+          "type": "object",
+          "patternProperties": {
+            ".+": {
+              "type": "string"
+            }
+          }
+        },
         "use-build-prefix": {
           "default": true,
           "description": "Add the wheel build path to the CMake prefix paths.",
diff --git a/src/scikit_build_core/settings/skbuild_model.py b/src/scikit_build_core/settings/skbuild_model.py
index 200915c1..6b3bbba8 100644
--- a/src/scikit_build_core/settings/skbuild_model.py
+++ b/src/scikit_build_core/settings/skbuild_model.py
@@ -93,6 +93,23 @@ class SearchSettings:
     Add the wheel build path to the CMake prefix paths.
     """
 
+    modules: Optional[Union[List[Path], Dict[str, Path]]] = 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
+    """
+    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)
+    """
+    Dict of package names and prefix paths. Populates `<Pkg>_ROOT`.
+    """
+
 
 @dataclasses.dataclass
 class NinjaSettings: