diff --git a/src/format/html/format-html-shared.ts b/src/format/html/format-html-shared.ts
index 6d63e73abd5..dbba131dc03 100644
--- a/src/format/html/format-html-shared.ts
+++ b/src/format/html/format-html-shared.ts
@@ -317,7 +317,8 @@ export const quartoDefaults = (format: Format) => {
         "code-copy-selector",
         format.metadata[kCodeCopy] === undefined ||
           format.metadata[kCodeCopy] === "hover"
-          ? '"pre.sourceCode:hover > "'
+          // ? '"div.sourceCode:hover > "'
+          ? '"div.code-copy-outer-scaffold:hover > "'
           : '""',
       ),
     ),
diff --git a/src/format/html/format-html.ts b/src/format/html/format-html.ts
index 0116419ce82..305de562c8c 100644
--- a/src/format/html/format-html.ts
+++ b/src/format/html/format-html.ts
@@ -750,12 +750,25 @@ function htmlFormatPostprocessor(
 
       // insert code copy button (with specfic attribute when inside a modal)
       if (codeCopy) {
-        code.classList.add("code-with-copy");
+        // the interaction of code copy button fixed position
+        // and scrolling overflow behavior requires a scaffold div to be inserted
+        // as a parent of the code block and the copy button both
+        // (see #13009, #5538, and #12787)
+        const outerScaffold = doc.createElement("div");
+        outerScaffold.classList.add("code-copy-outer-scaffold");
+
         const copyButton = createCodeCopyButton(doc, format);
         if (EmbedSourceModal && EmbedSourceModal.contains(code)) {
           copyButton.setAttribute("data-in-quarto-modal", "");
         }
-        code.appendChild(copyButton);
+        code.classList.add("code-with-copy");
+
+        const sourceCodeDiv = code.parentElement!;
+        const sourceCodeDivParent = code.parentElement?.parentElement;
+        sourceCodeDivParent!.replaceChild(outerScaffold, sourceCodeDiv);
+
+        outerScaffold.appendChild(sourceCodeDiv);
+        outerScaffold.appendChild(copyButton);
       }
 
       // insert example iframe
diff --git a/src/resources/formats/html/_quarto-rules.scss b/src/resources/formats/html/_quarto-rules.scss
index 4a4e9959f5e..f10cadb5a86 100644
--- a/src/resources/formats/html/_quarto-rules.scss
+++ b/src/resources/formats/html/_quarto-rules.scss
@@ -282,7 +282,7 @@ details > summary > p:only-child {
 }
 
 // codeCopy
-div.sourceCode {
+div.code-copy-outer-scaffold {
   position: relative;
 }
 
diff --git a/src/resources/formats/html/bootstrap/_bootstrap-rules.scss b/src/resources/formats/html/bootstrap/_bootstrap-rules.scss
index ed6dd280b9b..07d982073db 100644
--- a/src/resources/formats/html/bootstrap/_bootstrap-rules.scss
+++ b/src/resources/formats/html/bootstrap/_bootstrap-rules.scss
@@ -877,7 +877,8 @@ pre.sourceCode {
     border: none;
   }
   font-size: $code-block-font-size;
-  overflow-y: auto !important;
+  overflow-y: visible !important;
+  // overflow-y: auto !important;
   @if $code-block-bg {
     padding: $code-block-bg-padding;
   }
@@ -890,7 +891,8 @@ pre.sourceCode > code.sourceCode {
 }
 
 div.sourceCode {
-  position: relative;
+  overflow-y: hidden;
+  // position: relative;
 }
 
 .callout div.sourceCode {