diff --git a/CHANGELOG.md b/CHANGELOG.md
index aca2e6f200..ec7410ce6b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -24,6 +24,7 @@
 
 - Fix linting fail on nfcore_external_java_deps if nf_schema is used ([#2976](https://github.com/nf-core/tools/pull/2976))
 - Conda module linting: Include package name in log file ([#3014](https://github.com/nf-core/tools/pull/3014))
+- Remove defaults from conda `environment.yml` file. ([#3029](https://github.com/nf-core/tools/pull/3029))
 - Restructure pipeline tests and move pipeline linting into subfolder ([#3070](https://github.com/nf-core/tools/pull/3070))
 - Fix module linting warning for process_high_memory ([#3086](https://github.com/nf-core/tools/issues/3086))
 
diff --git a/nf_core/module-template/environment.yml b/nf_core/module-template/environment.yml
index dcf510affb..f234f85422 100644
--- a/nf_core/module-template/environment.yml
+++ b/nf_core/module-template/environment.yml
@@ -4,6 +4,5 @@ name: "{{ component_name_underscore }}"
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - "{{ bioconda if bioconda else 'YOUR-TOOL-HERE' }}"
diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
index eb9391b29a..8b156083f3 100644
--- a/nf_core/pipeline-template/modules.json
+++ b/nf_core/pipeline-template/modules.json
@@ -22,7 +22,7 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "20c03aede5a80ff520a905cea1f8ca121b5bb661",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
diff --git a/nf_core/pipeline-template/modules/nf-core/fastqc/environment.yml b/nf_core/pipeline-template/modules/nf-core/fastqc/environment.yml
index 1787b38a9a..0d5be45f26 100644
--- a/nf_core/pipeline-template/modules/nf-core/fastqc/environment.yml
+++ b/nf_core/pipeline-template/modules/nf-core/fastqc/environment.yml
@@ -2,6 +2,5 @@ name: fastqc
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::fastqc=0.12.1
diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml b/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml
index ca39fb67e2..329ddb4870 100644
--- a/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml
+++ b/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml
@@ -2,6 +2,5 @@ name: multiqc
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::multiqc=1.21
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index daa1c5e369..4a06efc984 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -102,7 +102,7 @@ profiles {
         podman.enabled          = false
         shifter.enabled         = false
         charliecloud.enabled    = false
-        conda.channels          = ['conda-forge', 'bioconda', 'defaults']
+        conda.channels          = ['conda-forge', 'bioconda']
         apptainer.enabled       = false
     }
     mamba {
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
index ac31f28f66..e770d91b97 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
@@ -102,7 +102,7 @@ def checkCondaChannels() {
 
     // Check that all channels are present
     // This channel list is ordered by required channel priority.
-    def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults']
+    def required_channels_in_order = ['conda-forge', 'bioconda']
     def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean
 
     // Check that they are in the right order
diff --git a/nf_core/utils.py b/nf_core/utils.py
index 96c16130ca..663efb6b46 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -654,7 +654,7 @@ def anaconda_package(dep, dep_channels=None):
     """
 
     if dep_channels is None:
-        dep_channels = ["conda-forge", "bioconda", "defaults"]
+        dep_channels = ["conda-forge", "bioconda"]
 
     # Check if each dependency is the latest available version
     if "=" in dep:
diff --git a/tests/test_utils.py b/tests/test_utils.py
index 0d012716a9..bde561d95e 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -81,7 +81,7 @@ def testload_pipeline_config(self):
     # def test_load_conda_env(self):
     #     """Load the pipeline Conda environment.yml file"""
     #     self.pipeline_obj._load_conda_environment()
-    #     assert self.pipeline_obj.conda_config["channels"] == ["conda-forge", "bioconda", "defaults"]
+    #     assert self.pipeline_obj.conda_config["channels"] == ["conda-forge", "bioconda"]
 
     def test_list_files_git(self):
         """Test listing pipeline files using `git ls`"""