diff --git a/CHANGELOG.md b/CHANGELOG.md
index 105d01276a..0eaae0b40d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,10 @@
 
 ## v1.10dev
 
+### Template
+
+* Isolate R library paths to those in container [#541](https://github.com/nf-core/tools/issues/541)
+
 ### Linting
 
 * Refactored PR branch tests to be a little clearer.
diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/Dockerfile b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/Dockerfile
index 69d24cdc31..b1e0c19a74 100644
--- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/Dockerfile
+++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/Dockerfile
@@ -11,3 +11,7 @@ ENV PATH /opt/conda/envs/{{ cookiecutter.name_noslash }}-{{ cookiecutter.version
 
 # Dump the details of the installed packages to a file for posterity
 RUN conda env export --name {{ cookiecutter.name_noslash }}-{{ cookiecutter.version }} > {{ cookiecutter.name_noslash }}-{{ cookiecutter.version }}.yml
+
+# Instruct R processes to use these empty files instead of clashing with a local version
+RUN touch .Rprofile
+RUN touch .Renviron
diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config
index c8d4ea682a..e9ed7d669e 100644
--- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config
+++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config
@@ -78,9 +78,11 @@ if (!params.igenomes_ignore) {
   includeConfig 'conf/igenomes.config'
 }
 
-// Export this variable to prevent local Python libraries from conflicting with those in the container
+// Export these variables to prevent local Python/R libraries from conflicting with those in the container
 env {
   PYTHONNOUSERSITE = 1
+  R_PROFILE_USER = "/.Rprofile"
+  R_ENVIRON_USER = "/.Renviron"
 }
 
 // Capture exit codes from upstream processes when piping