diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index c6ba17b..1596829 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -68,6 +68,29 @@ jobs:
           # We also remove the surplus entry for the classes with spaces
           sed -i 's/<code><a href="\(\w\+\)\.html">\w\+\.[a-zA-Z_ ]\+<\/a><\/code>//g' docs/reference/index.html
 
+      - name: Remove question marks from auto-linked references
+        run: |
+          # The only way to auto-link R6 objects is by prepending af `?` to the code block
+          # For specific functions in an R6 class, it is possible to prepend the parent class `?parent$function()`
+
+          # Here we filter out these prepended blocks to generate a cleaner documentation.
+
+          # Fixing "?R6class"
+          # The links to the internal R6 classes have the following format when generated by pkgdown:
+          # <a href="../reference/FeatureHandler.html">?FeatureHandler</a>
+          # We remove the question mark to make the link cleaner
+          # regex: <a href="\.\.\/([\/\w]+.html)">\?(\w+)<\/a>
+          find docs -type f -exec sed -i 's/<a href="\.\.\/\([\/\w]\+\.html\)">\?\(\w\+\)<\/a>/<a href="\1">\2<\/a>/g' {} +
+
+          # Fixing "?R6class$function()"
+          # pkgdown does not generate links for this type of reference, so we need to create the link fully manually
+          # The code has the following format when generated by pkgdown
+          # <code>?DiseasystoreBase$available_observables</code>
+          # We need to manually create the link to the function
+          # regex: <code>\?(\w+)\$()(\w+\(\))<\/code>
+          # Target: <a href="../reference/DiseasystoreBase.html#method-DiseasystoreBase-get_feature"><code>get_feature()</code></a>
+          find docs -type f -exec sed -i 's/<code>\?\(\w\+\)\$\(\w\+\(\)\)<\/code>/<a href="\.\.\/reference\/\1.html#method-\1-\2"><code>\2<\/code><\/a>/g' {} +
+
       - name: Upload artifact
         uses: actions/upload-artifact@v4
         with:
diff --git a/workflows/README.md b/workflows/README.md
index 7b74f2f..cd6bbf5 100644
--- a/workflows/README.md
+++ b/workflows/README.md
@@ -119,10 +119,16 @@ If this generate changes the `.Rd` files, it will commit the updated documentati
 #### Trigger
 Pushes or pull requests to the main branch if there are changes to any file in the `R/`, `man/` or `vignette/` folders.
 
-Special triggering on creation of a `release`
+Special triggering on creation of a `release`.
 
 #### Function
-Generates the `pkgdown` documentation for your package
+Generates the `pkgdown` documentation for your package.
+
+> [!IMPORTANT]
+> This workflow runs additional formatting of the pkgdown documentation.
+> Specifically, it adds auto-linking to R6 object
+> - `?MyR6Class` is rendered without the `?` and links to `MyR6Class`.
+> - `?MyR6Class$method()` is rendered as `method()` and links to the method of `MyR6Class`
 
 #### Outcome
 The output of `pkgdown` is stored as an artifact on github.