diff --git a/CHANGELOG.md b/CHANGELOG.md
index 40450bc51d..8aa76b8f77 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,6 +14,7 @@
 - Remove `pyproject.toml` from template root
 - Shorten lines in pipeline template ([#2908](https://github.com/nf-core/tools/pull/2908))
 - Permanently activated pipeline-specific institutional configs support for all pipelines without need for manual intervention ([#2936](https://github.com/nf-core/tools/pull/2936))
+- Handles multiple DOIs + doi.org resolver from manifest.doi ([#2946](https://github.com/nf-core/tools/pull/2946))
 - Update included components ([#2949](https://github.com/nf-core/tools/pull/2949))
 
 ### Linting
diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
index e02a113755..a4bfb9f8be 100644
--- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
@@ -243,8 +243,16 @@ def methodsDescriptionText(mqc_methods_yaml) {
     meta["manifest_map"] = workflow.manifest.toMap()
 
     // Pipeline DOI
-    meta["doi_text"] = meta.manifest_map.doi ? "(doi: <a href=\'https://doi.org/${meta.manifest_map.doi}\'>${meta.manifest_map.doi}</a>)" : ""
-    meta["nodoi_text"] = meta.manifest_map.doi ? "": "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
+    if (meta.manifest_map.doi) {
+        // Using a loop to handle multiple DOIs
+        // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
+        // Removing ` ` since the manifest.doi is a string and not a proper list
+        def temp_doi_ref = ""
+        String[] manifest_doi = meta.manifest_map.doi.tokenize(",")
+        for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: <a href=\'https://doi.org/${doi_ref.replace("https://doi.org/", "").replace(" ", "")}\'>${doi_ref.replace("https://doi.org/", "").replace(" ", "")}</a>), "
+        meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2)
+    } else meta["doi_text"] = ""
+    meta["nodoi_text"] = meta.manifest_map.doi ? "" : "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
 
     // Tool references
     meta["tool_citations"] = ""