diff --git a/src/pydata_sphinx_theme/translator.py b/src/pydata_sphinx_theme/translator.py
index eb2046bd4..caed17565 100644
--- a/src/pydata_sphinx_theme/translator.py
+++ b/src/pydata_sphinx_theme/translator.py
@@ -1,8 +1,10 @@
 """A custom Sphinx HTML Translator for Bootstrap layout."""
 
 import types
+from functools import partial
 
 import sphinx
+from docutils.nodes import Element
 from packaging.version import Version
 from sphinx.application import Sphinx
 from sphinx.ext.autosummary import autosummary_table
@@ -59,6 +61,86 @@ def visit_table(self, node):
         tag = self.starttag(node, "table", CLASS=" ".join(classes), **atts)
         self.body.append(tag)
 
+    # NOTE: `visit_section`, `visit_desc_signature` & `visit_reference` are extended
+    # here to resolve #1026 & #1207. There is an open issue with Sphinx to address this:
+    # https://github.com/sphinx-doc/sphinx/issues/11208
+    # If the issue is resolved within Sphinx, these methods can be removed.
+
+    def visit_section(self, node):
+        """Handle section nodes to replace dots with underscores.
+
+        This will modify the ``id`` of HTML ``<section>`` tags, where Python modules
+        are documented. Replacing dots with underscores allows the tags to be recognized
+        as navigation targets by ScrollSpy.
+        """
+        if "ids" in node:
+            node["ids"] = [id_.replace(".", "_") for id_ in node["ids"]]
+        super().visit_section(node)
+
+    def visit_desc_signature(self, node):
+        """Handle function & method signature nodes to replace dots with underscores.
+
+        This will modify the ``id`` attribute of HTML ``<dt>`` & ``<dd>`` tags, where
+        Python functions are documented. Replacing dots with underscores allows the tags
+        to be recognized as navigation targets by ScrollSpy.
+        """
+        if "ids" in node:
+            ids = node["ids"]
+            for i, id_ in enumerate(ids):
+                ids[i] = id_.replace(".", "_")
+        super().visit_desc_signature(node)
+
+    def visit_reference(self, node):
+        """Handle reference nodes to replace dots with underscores.
+
+        This will modify the ``href`` attribute of any internal HTML ``<a>`` tags, e.g.
+        the sidebar navigation links.
+        """
+        try:
+            # We are only interested in internal anchor references
+            internal, anchorname = node["internal"], node["anchorname"]
+            if internal and anchorname.startswith("#") and "." in anchorname:
+                # Get the root node of the current document
+                document = self.builder.env.get_doctree(self.builder.current_docname)
+
+                # Get the target anchor ID
+                target_id = anchorname.lstrip("#")
+                sanitized_id = target_id.replace(".", "_")
+                # Update the node `href`
+                node["refuri"] = node["anchorname"] = "#" + sanitized_id
+
+                # Define a search condition to find the target node by ID
+                def find_target(search_id, node):
+                    return (
+                        isinstance(node, Element)
+                        and ("ids" in node)
+                        and (search_id in node["ids"])
+                    )
+
+                # NOTE: Replacing with underscores creates the possibility for
+                # conflicting references. We should check for these and warn the
+                # user if any are found.
+                if any(document.traverse(condition=partial(find_target, sanitized_id))):
+                    logger.warning(
+                        f'Sanitized reference "{sanitized_id}" for "{target_id}" '
+                        "conflicts with an existing reference!"
+                    )
+
+                # Find nodes with the given ID (there should only be one)
+                targets = document.traverse(condition=partial(find_target, target_id))
+                # Replace dots with underscores in the target node ID
+                for target in targets:
+                    # NOTE: By itself, modifying the target `ids` here seems to be
+                    # insufficient, however it helps ensure that the reference `refuri`
+                    # and target `ids` remain consistent during the build process
+                    target["ids"] = [
+                        sanitized_id if id_ == target_id else id_
+                        for id_ in target["ids"]
+                    ]
+        except KeyError:
+            pass
+        super().visit_reference(node)
+
 
 def setup_translators(app: Sphinx):
     """Add bootstrap HTML functionality if we are using an HTML translator.