diff --git a/CHANGELOG.md b/CHANGELOG.md
index d8c5d89f5d..be6d5820d7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -18,6 +18,7 @@
 
 - Fix the syntax of github_output in GitHub actions ([#2114](https://github.com/nf-core/tools/pull/2114))
 - Fix a bug introduced in 2.7 that made pipelines hang ([#2132](https://github.com/nf-core/tools/issues/2132))
+- Explicitly disable `conda` when a container profile ([#2140](https://github.com/nf-core/tools/pull/2140))
 
 ### Linting
 
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 5cbb076b46..cc591a54e5 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -102,6 +102,7 @@ profiles {
     docker {
         docker.enabled         = true
         docker.userEmulation   = true
+        conda.enabled          = false
         singularity.enabled    = false
         podman.enabled         = false
         shifter.enabled        = false
@@ -113,6 +114,7 @@ profiles {
     singularity {
         singularity.enabled    = true
         singularity.autoMounts = true
+        conda.enabled          = false
         docker.enabled         = false
         podman.enabled         = false
         shifter.enabled        = false
@@ -120,6 +122,7 @@ profiles {
     }
     podman {
         podman.enabled         = true
+        conda.enabled          = false
         docker.enabled         = false
         singularity.enabled    = false
         shifter.enabled        = false
@@ -127,6 +130,7 @@ profiles {
     }
     shifter {
         shifter.enabled        = true
+        conda.enabled          = false
         docker.enabled         = false
         singularity.enabled    = false
         podman.enabled         = false
@@ -134,6 +138,7 @@ profiles {
     }
     charliecloud {
         charliecloud.enabled   = true
+        conda.enabled          = false
         docker.enabled         = false
         singularity.enabled    = false
         podman.enabled         = false