diff --git a/CHANGELOG.md b/CHANGELOG.md
index e753f935d..fe3025a4f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -19,6 +19,7 @@ Special thanks to the following for their contributions to the release:
 - [PR #1463](https://github.com/nf-core/rnaseq/pull/1463) - Move channel operations outside of the onComplete() block
 - [PR #1467](https://github.com/nf-core/rnaseq/pull/1467) - Add test suite for UMI handling functionality
 - [PR #1466](https://github.com/nf-core/rnaseq/pull/1466) - Factor out UMI handling
+- [PR #1459](https://github.com/nf-core/rnaseq/pull/1466) - Remove reference to unused "skip_sample_count" value in email templates
 
 ### Software dependencies
 
diff --git a/assets/email_template.html b/assets/email_template.html
index dc46d39ee..e4639cdb6 100644
--- a/assets/email_template.html
+++ b/assets/email_template.html
@@ -34,25 +34,6 @@ <h4 style="margin-top: 0; color: inherit">nf-core/rnaseq execution completed uns
         <p>The full error message was:</p>
         <pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0">${errorReport}</pre>
       </div>
-      """ } else if(skip_sample_count > 0) { out << """
-      <div
-        style="
-          color: #856404;
-          background-color: #fff3cd;
-          border-color: #ffeeba;
-          padding: 15px;
-          margin-bottom: 20px;
-          border: 1px solid transparent;
-          border-radius: 4px;
-        "
-      >
-        <h4 style="margin-top: 0; color: inherit">nf-core/rnaseq execution completed with warnings!</h4>
-        <p>
-          The pipeline finished successfully, but samples were skipped. Please check warnings at the top of the MultiQC report.
-        </p>
-        <p></p>
-      </div>
-
       """ } else { out << """
       <div
         style="
diff --git a/assets/email_template.txt b/assets/email_template.txt
index 8789fd8ae..ea2df520d 100644
--- a/assets/email_template.txt
+++ b/assets/email_template.txt
@@ -17,13 +17,6 @@ The full error message was:
 
 ${errorReport}
 """
-} else if (skip_sample_count > 0) {
-    out << """##################################################
-## nf-core/rnaseq execution completed with warnings ##
-##################################################
-The pipeline finished successfully, but samples were skipped.
-Please check warnings at the top of the MultiQC report.
-"""
 } else {
     out << "## nf-core/rnaseq execution completed successfully! ##"
 }