diff --git a/docs/docs/structure.md b/docs/docs/structure.md
index d3c36428..78e656b7 100644
--- a/docs/docs/structure.md
+++ b/docs/docs/structure.md
@@ -315,7 +315,6 @@ You can write reports in markdown and put them in `outputs/reports` and referenc
 ├── requirements.txt                 |  PYTHON DEPENDENCIES NEEDED TO RUN THE CODE
 ├── requirements_dev.txt             |  PYTHON DEV DEPENDENCIES (e.g. building docs/running tests)
 ├── inputs/                          |  INPUTS (should be immutable)
-├── jupytext.toml                    |  JUPYTEXT CONFIGURATION
 ├── LICENSE                          |
 ├── outputs/                          |  OUTPUTS PRODUCED FROM THE PROJECT
 ├── Makefile                         |  TASKS TO COORDINATE PROJECT (`make` shows available commands)
diff --git a/{{ cookiecutter.repo_name }}/.github/pull_request_template.md b/{{ cookiecutter.repo_name }}/.github/pull_request_template.md
index 8a66a687..2484e2e8 100644
--- a/{{ cookiecutter.repo_name }}/.github/pull_request_template.md	
+++ b/{{ cookiecutter.repo_name }}/.github/pull_request_template.md	
@@ -14,7 +14,6 @@ Please pay special attention to ...
 
 # Checklist:
 
-- [ ] I have refactored my code out from `notebooks/`
 - [ ] I have checked the code runs
 - [ ] I have tested the code
 - [ ] I have run `pre-commit` and addressed any issues not automatically fixed
diff --git a/{{ cookiecutter.repo_name }}/.gitignore b/{{ cookiecutter.repo_name }}/.gitignore
index 50145824..fd1b162c 100644
--- a/{{ cookiecutter.repo_name }}/.gitignore	
+++ b/{{ cookiecutter.repo_name }}/.gitignore	
@@ -20,9 +20,6 @@ research_daps/
 metaflow.s3.*
 .run_id
 
-# Notebooks (use jupytext instead!)
-*.ipynb
-
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
diff --git a/{{ cookiecutter.repo_name }}/jupytext.toml b/{{ cookiecutter.repo_name }}/jupytext.toml
deleted file mode 100644
index b2a5c34c..00000000
--- a/{{ cookiecutter.repo_name }}/jupytext.toml	
+++ /dev/null
@@ -1,10 +0,0 @@
-# Jupytext config file
-
-# Always pair ipynb notebooks to py:percent files
-default_jupytext_formats = "ipynb,py:percent"
-
-# Comment out magics (allows code formatting)
-comment_magics = true
-
-# Strip cell-level metadata (avoid polluting git diffs)
-default_cell_metadata_filter = "-all"
diff --git a/{{ cookiecutter.repo_name }}/requirements_dev.txt b/{{ cookiecutter.repo_name }}/requirements_dev.txt
index aa382034..ecace4f7 100644
--- a/{{ cookiecutter.repo_name }}/requirements_dev.txt	
+++ b/{{ cookiecutter.repo_name }}/requirements_dev.txt	
@@ -1,5 +1,4 @@
 ipykernel
-jupytext
 flake8
 flake8-black
 flake8-import-order