diff --git a/CHANGELOG.md b/CHANGELOG.md
index 313be748b..bb897d76c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -63,6 +63,7 @@
 - Remove toList() channel operation from inside onComplete block ([#3304](https://github.com/nf-core/tools/pull/3304))
 - build: Setup VS Code tests ([#3292](https://github.com/nf-core/tools/pull/3292))
 - Don't break gitpod.yml with template string ([#3332](https://github.com/nf-core/tools/pull/3332))
+- rocrate: remove duplicated entries for name and version ([#3333](https://github.com/nf-core/tools/pull/3333))
 
 ### Version updates
 
diff --git a/nf_core/pipelines/rocrate.py b/nf_core/pipelines/rocrate.py
index 915f203f0..21df0513a 100644
--- a/nf_core/pipelines/rocrate.py
+++ b/nf_core/pipelines/rocrate.py
@@ -216,6 +216,9 @@ def set_main_entity(self, main_entity_filename: str):
         )
         self.crate.mainEntity.append_to("version", self.version, compact=True)
 
+        # remove duplicate entries for version
+        self.crate.mainEntity["version"] = list(set(self.crate.mainEntity["version"]))
+
         # get keywords from nf-core website
         remote_workflows = requests.get("https://nf-co.re/pipelines.json").json()["remote_workflows"]
         # go through all remote workflows and find the one that matches the pipeline name
@@ -236,6 +239,9 @@ def set_main_entity(self, main_entity_filename: str):
         self.crate.mainEntity.append_to("license", self.crate.license)
         self.crate.mainEntity.append_to("name", self.crate.name)
 
+        # remove duplicate entries for name
+        self.crate.mainEntity["name"] = list(set(self.crate.mainEntity["name"]))
+
         if "dev" in self.version:
             self.crate.creativeWorkStatus = "InProgress"
         else: