diff --git a/src/extensions/score_draw_uml_funcs/__init__.py b/src/extensions/score_draw_uml_funcs/__init__.py
index 8276b80f..d4a95f39 100644
--- a/src/extensions/score_draw_uml_funcs/__init__.py
+++ b/src/extensions/score_draw_uml_funcs/__init__.py
@@ -60,7 +60,8 @@
 
 
 def setup(app: Sphinx) -> dict[str, object]:
-    app.config.needs_render_context = draw_uml_function_context
+    for key, value in draw_uml_function_context.items():
+        app.config.needs_render_context.setdefault(key, value)
     return {
         "version": "0.1",
         "parallel_read_safe": True,
diff --git a/src/extensions/score_layout/__init__.py b/src/extensions/score_layout/__init__.py
index 6d54f0b7..62ec548f 100644
--- a/src/extensions/score_layout/__init__.py
+++ b/src/extensions/score_layout/__init__.py
@@ -18,6 +18,8 @@
 import sphinx_options
 from sphinx.application import Sphinx
 
+from src.helper_lib import config_setdefault
+
 logger = logging.getLogger(__name__)
 
 
@@ -35,11 +37,18 @@ def setup(app: Sphinx) -> dict[str, str | bool]:
 def update_config(app: Sphinx, _config: Any):
     logger.debug("score_layout update_config called")
 
-    app.config.needs_layouts = sphinx_options.needs_layouts
-    app.config.needs_global_options = sphinx_options.needs_global_options
-    app.config.html_theme = html_options.html_theme
-    app.config.html_context = html_options.return_html_context(app)
-    app.config.html_theme_options = html_options.return_html_theme_options(app)
+    # Merge: user's entries take precedence over our defaults
+    app.config.needs_layouts = {**sphinx_options.needs_layouts, **app.config.needs_layouts}
+    app.config.needs_global_options = {
+        **sphinx_options.needs_global_options,
+        **app.config.needs_global_options,
+    }
+    config_setdefault(app.config, "html_theme", html_options.html_theme)
+    app.config.html_context = {**html_options.return_html_context(app), **app.config.html_context}
+    app.config.html_theme_options = {
+        **html_options.return_html_theme_options(app),
+        **app.config.html_theme_options,
+    }
 
     logger.debug(f"score_layout __file__: {__file__}")
 
@@ -49,7 +58,7 @@ def update_config(app: Sphinx, _config: Any):
     app.config.html_static_path.append(str(score_layout_path / "assets"))
 
     puml = score_layout_path / "assets" / "puml-theme-score.puml"
-    app.config.needs_flow_configs = {"score_config": f"!include {puml}"}
+    app.config.needs_flow_configs.setdefault("score_config", f"!include {puml}")
 
     app.add_css_file("css/score.css", priority=500)
     app.add_css_file("css/score_needs.css", priority=500)
diff --git a/src/extensions/score_metamodel/__init__.py b/src/extensions/score_metamodel/__init__.py
index 0a6c4dae..fddff21f 100644
--- a/src/extensions/score_metamodel/__init__.py
+++ b/src/extensions/score_metamodel/__init__.py
@@ -18,6 +18,8 @@
 
 from sphinx.application import Sphinx
 from sphinx_needs import logging
+
+from src.helper_lib import config_setdefault
 from sphinx_needs.data import NeedsView, SphinxNeedsData
 from sphinx_needs.need_item import NeedItem
 
@@ -231,25 +233,25 @@ def postprocess_need_links(needs_types_list: list[ScoreNeedType]):
 
 def setup(app: Sphinx) -> dict[str, str | bool]:
     app.add_config_value("external_needs_source", "", rebuild="env")
-    app.config.needs_id_required = True
-    app.config.needs_id_regex = "^[A-Za-z0-9_-]{6,}"
+    config_setdefault(app.config, "needs_id_required", True)
+    config_setdefault(app.config, "needs_id_regex", "^[A-Za-z0-9_-]{6,}")
 
     # load metamodel.yaml via ruamel.yaml
     metamodel = load_metamodel_data()
 
-    # Assign everything to Sphinx config
-    app.config.needs_types = metamodel.needs_types
-    app.config.needs_extra_links = metamodel.needs_extra_links
-    app.config.needs_extra_options = metamodel.needs_extra_options
+    # Extend sphinx-needs config rather than overwriting
+    app.config.needs_types += metamodel.needs_types
+    app.config.needs_extra_links += metamodel.needs_extra_links
+    app.config.needs_extra_options += metamodel.needs_extra_options
     app.config.graph_checks = metamodel.needs_graph_check
     app.config.prohibited_words_checks = metamodel.prohibited_words_checks
 
     # app.config.stop_words = metamodel["stop_words"]
     # app.config.weak_words = metamodel["weak_words"]
     # Ensure that 'needs.json' is always build.
-    app.config.needs_build_json = True
-    app.config.needs_reproducible_json = True
-    app.config.needs_json_remove_defaults = True
+    config_setdefault(app.config, "needs_build_json", True)
+    config_setdefault(app.config, "needs_reproducible_json", True)
+    config_setdefault(app.config, "needs_json_remove_defaults", True)
 
     # sphinx-collections runs on default prio 500.
     # We need to populate the sphinx-collections config before that happens.
diff --git a/src/extensions/score_plantuml.py b/src/extensions/score_plantuml.py
index 3dbbd138..b46b51aa 100644
--- a/src/extensions/score_plantuml.py
+++ b/src/extensions/score_plantuml.py
@@ -29,7 +29,7 @@
 from sphinx.application import Sphinx
 from sphinx.util import logging
 
-from src.helper_lib import get_runfiles_dir
+from src.helper_lib import config_setdefault, get_runfiles_dir
 
 logger = logging.getLogger(__name__)
 
@@ -53,10 +53,11 @@ def find_correct_path(runfiles: Path) -> Path:
 
 
 def setup(app: Sphinx):
-    app.config.plantuml = str(find_correct_path(get_runfiles_dir()))
-    app.config.plantuml_output_format = "svg_obj"
-    app.config.plantuml_syntax_error_image = True
-    app.config.needs_build_needumls = "_plantuml_sources"
+    if not app.config.plantuml:
+        app.config.plantuml = str(find_correct_path(get_runfiles_dir()))
+    config_setdefault(app.config, "plantuml_output_format", "svg_obj")
+    config_setdefault(app.config, "plantuml_syntax_error_image", True)
+    config_setdefault(app.config, "needs_build_needumls", "_plantuml_sources")
 
     logger.debug(f"PlantUML binary found at {app.config.plantuml}")
 
diff --git a/src/extensions/score_source_code_linker/__init__.py b/src/extensions/score_source_code_linker/__init__.py
index 094ebf4a..cf9843dc 100644
--- a/src/extensions/score_source_code_linker/__init__.py
+++ b/src/extensions/score_source_code_linker/__init__.py
@@ -173,14 +173,15 @@ def setup_source_code_linker(app: Sphinx, ws_root: Path):
 
     # Define need_string_links here to not have it in conf.py
     # source_code_link and testlinks have the same schema
-    app.config.needs_string_links = {
-        "source_code_linker": {
+    app.config.needs_string_links.setdefault(
+        "source_code_linker",
+        {
             "regex": r"(?P<url>.+)<>(?P<name>.+)",
             "link_url": "{{url}}",
             "link_name": "{{name}}",
             "options": ["source_code_link", "testlink"],
         },
-    }
+    )
 
     score_sourcelinks_json = os.environ.get("SCORE_SOURCELINKS")
     if score_sourcelinks_json:
diff --git a/src/extensions/score_sphinx_bundle/__init__.py b/src/extensions/score_sphinx_bundle/__init__.py
index d30df6c3..9dfd8680 100644
--- a/src/extensions/score_sphinx_bundle/__init__.py
+++ b/src/extensions/score_sphinx_bundle/__init__.py
@@ -12,6 +12,8 @@
 # *******************************************************************************
 from sphinx.application import Sphinx
 
+from src.helper_lib import config_setdefault
+
 # Note: order matters!
 # Extensions are loaded in this order.
 # e.g. plantuml MUST be loaded before sphinx-needs
@@ -33,43 +35,41 @@
 
 
 def setup(app: Sphinx) -> dict[str, object]:
-    app.config.html_copy_source = False
-    app.config.html_show_sourcelink = False
+    config_setdefault(app.config, "html_copy_source", False)
+    config_setdefault(app.config, "html_show_sourcelink", False)
 
     # Global settings
     # Note: the "sub-extensions" also set their own config values
 
     # Same as current VS Code extension
-    app.config.mermaid_version = "11.6.0"
-
-    # enable "..."-syntax in markdown
-    app.config.myst_enable_extensions = ["colon_fence"]
+    config_setdefault(app.config, "mermaid_version", "11.6.0")
 
-    app.config.exclude_patterns = [
-        # The following entries are not required when building the documentation via
-        # 'bazel build //:docs', as that command runs in a sandboxed environment.
-        # However, when building the documentation via 'bazel run //:docs' or esbonio,
-        # these entries are required to prevent the build from failing.
-        "bazel-*",
-        ".venv*",
-    ]
+    # The following entries are not required when building the documentation via
+    # 'bazel build //:docs', as that command runs in a sandboxed environment.
+    # However, when building the documentation via 'bazel run //:docs' or esbonio,
+    # these entries are required to prevent the build from failing.
+    app.config.exclude_patterns += ["bazel-*", ".venv*"]
 
     # Enable markdown rendering
-    app.config.source_suffix = {
-        ".rst": "restructuredtext",
-        ".md": "markdown",
-    }
+    app.config.source_suffix.setdefault(".rst", "restructuredtext")
+    app.config.source_suffix.setdefault(".md", "markdown")
 
-    app.config.templates_path = ["templates"]
+    if "templates" not in app.config.templates_path:
+        app.config.templates_path += ["templates"]
 
-    app.config.numfig = True
+    config_setdefault(app.config, "numfig", True)
 
-    app.config.author = "S-CORE"
+    if not app.config.author:
+        app.config.author = "S-CORE"
 
     # Load the actual extensions list
     for e in score_extensions:
         app.setup_extension(e)
 
+    # enable "..."-syntax in markdown — must come after myst_parser is loaded above
+    if "colon_fence" not in app.config.myst_enable_extensions:
+        app.config.myst_enable_extensions = set(app.config.myst_enable_extensions) | {"colon_fence"}
+
     return {
         "version": "3.0.0",
         # Keep this in sync with the score_docs_as_code version in MODULE.bazel
diff --git a/src/extensions/score_sync_toml/__init__.py b/src/extensions/score_sync_toml/__init__.py
index 79ebfb7a..069e017c 100644
--- a/src/extensions/score_sync_toml/__init__.py
+++ b/src/extensions/score_sync_toml/__init__.py
@@ -14,6 +14,8 @@
 
 from sphinx.application import Sphinx
 
+from src.helper_lib import config_setdefault
+
 
 def setup(app: Sphinx) -> dict[str, str | bool]:
     """
@@ -22,29 +24,31 @@ def setup(app: Sphinx) -> dict[str, str | bool]:
     See https://needs-config-writer.useblocks.com
     """
 
-    app.config.needscfg_outpath = "ubproject.toml"
+    config_setdefault(app.config, "needscfg_outpath", "ubproject.toml")
     """Write to the confdir directory."""
 
-    app.config.needscfg_overwrite = True
+    config_setdefault(app.config, "needscfg_overwrite", True)
     """Any changes to the shared/local configuration updates the generated config."""
 
-    app.config.needscfg_write_all = True
+    config_setdefault(app.config, "needscfg_write_all", True)
     """Write full config, so the final configuration is visible in one file."""
 
-    app.config.needscfg_exclude_defaults = True
+    config_setdefault(app.config, "needscfg_exclude_defaults", True)
     """Exclude default values from the generated configuration."""
 
     # This is disabled for right now as it causes a lot of issues
     # While we are not using the generated file anywhere
-    app.config.needscfg_warn_on_diff = False
+    config_setdefault(app.config, "needscfg_warn_on_diff", False)
     """Running Sphinx with -W will fail the CI for uncommitted TOML changes."""
 
-    app.config.needscfg_merge_toml_files = [
-        str(Path(__file__).parent / "shared.toml"),
-    ]
+    app.config.needscfg_merge_toml_files = (
+        app.config.needscfg_merge_toml_files or []
+    ) + [str(Path(__file__).parent / "shared.toml")]
     """Merge the static TOML file into the generated configuration."""
 
-    app.config.needscfg_relative_path_fields = [
+    app.config.needscfg_relative_path_fields = (
+        app.config.needscfg_relative_path_fields or []
+    ) + [
         "needs_external_needs[*].json_path",
         {
             "field": "needs_flow_configs.score_config",
diff --git a/src/helper_lib/__init__.py b/src/helper_lib/__init__.py
index 156a50fc..b48536c5 100644
--- a/src/helper_lib/__init__.py
+++ b/src/helper_lib/__init__.py
@@ -15,13 +15,25 @@
 import subprocess
 import sys
 from pathlib import Path
+from typing import Any
 
 from runfiles import Runfiles
+from sphinx.config import Config
 from sphinx_needs.logging import get_logger
 
 LOGGER = get_logger(__name__)
 
 
+def config_setdefault(config: Config, name: str, value: Any) -> None:
+    """Set a Sphinx config value only if the user hasn't explicitly set it in conf.py."""
+
+    # Sphinx has no public API for this check. We use ``_raw_config`` which is the
+    # de-facto standard across the ecosystem (Furo, RTD-theme, etc.). If Sphinx
+    # ever adds a public alternative, update this single function.
+    if name not in config._raw_config:
+        setattr(config, name, value)
+
+
 def find_ws_root() -> Path | None:
     """
     Find the current MODULE.bazel workspace root directory.
diff --git a/src/helper_lib/test_helper_lib.py b/src/helper_lib/test_helper_lib.py
index 83bbc30e..9878bdbd 100644
--- a/src/helper_lib/test_helper_lib.py
+++ b/src/helper_lib/test_helper_lib.py
@@ -18,6 +18,7 @@
 import pytest
 
 from src.helper_lib import (
+    config_setdefault,
     get_current_git_hash,
     get_github_repo_info,
     get_runfiles_dir,
@@ -25,6 +26,26 @@
 )
 
 
+class _FakeConfig:
+    """Minimal stand-in for sphinx.config.Config sufficient to test config_setdefault."""
+
+    def __init__(self, raw: dict):
+        self._raw_config = raw
+
+
+def test_config_setdefault_sets_when_not_in_raw_config():
+    cfg = _FakeConfig(raw={})
+    config_setdefault(cfg, "html_copy_source", False)
+    assert cfg.html_copy_source is False
+
+
+def test_config_setdefault_does_not_overwrite_user_value():
+    cfg = _FakeConfig(raw={"html_copy_source": True})
+    cfg.html_copy_source = True
+    config_setdefault(cfg, "html_copy_source", False)
+    assert cfg.html_copy_source is True
+
+
 @pytest.fixture
 def temp_dir():
     """Create a temporary directory for tests."""