diff --git a/docs/nipoppy/cli_note.md b/docs/nipoppy/cli_note.md
new file mode 100644
index 00000000..30a7b939
--- /dev/null
+++ b/docs/nipoppy/cli_note.md
@@ -0,0 +1,10 @@
+!!! note "Nipoppy docs are moving"
+
+    Nipoppy is undergoing a major refactor to move from scripts to a 
+    command-line interface (CLI) and Python API. The new documentation website
+    (work in progress) can be found at
+    [https://nipoppy.readthedocs.io/](https://nipoppy.readthedocs.io/).
+
+    If you are using the (soon-to-be legacy) scripts from Nipoppy 0.1.0, this is
+    still the correct place to be. But we encourage you to check out the new
+    website!
diff --git a/docs/nipoppy/code_org.md b/docs/nipoppy/code_org.md
index 765acbd0..7963589d 100644
--- a/docs/nipoppy/code_org.md
+++ b/docs/nipoppy/code_org.md
@@ -1,3 +1,7 @@
+{%
+    include-markdown "nipoppy/cli_note.md"
+%}
+
 ## Code organization
 
 ---
diff --git a/docs/nipoppy/configs.md b/docs/nipoppy/configs.md
index f71c7b86..504a6987 100644
--- a/docs/nipoppy/configs.md
+++ b/docs/nipoppy/configs.md
@@ -1,3 +1,7 @@
+{%
+    include-markdown "nipoppy/cli_note.md"
+%}
+
 ## Global files
 
 ---
diff --git a/docs/nipoppy/data_org.md b/docs/nipoppy/data_org.md
index 61f87a6e..b3fec387 100644
--- a/docs/nipoppy/data_org.md
+++ b/docs/nipoppy/data_org.md
@@ -1,3 +1,7 @@
+{%
+    include-markdown "nipoppy/cli_note.md"
+%}
+
 ## Data organization
 
 ---
diff --git a/docs/nipoppy/glossary.md b/docs/nipoppy/glossary.md
index cc3a3e9d..6a72274c 100644
--- a/docs/nipoppy/glossary.md
+++ b/docs/nipoppy/glossary.md
@@ -1,3 +1,7 @@
+{%
+    include-markdown "nipoppy/cli_note.md"
+%}
+
 ## Glossary
 
 This page lists some definitions for important/recurring terms used in the Nipoppy framework.
diff --git a/docs/nipoppy/installation.md b/docs/nipoppy/installation.md
index f93d746c..c343829a 100644
--- a/docs/nipoppy/installation.md
+++ b/docs/nipoppy/installation.md
@@ -1,3 +1,7 @@
+{%
+    include-markdown "nipoppy/cli_note.md"
+%}
+
 ## Code installation and dataset setup
 
 ---
diff --git a/docs/nipoppy/overview.md b/docs/nipoppy/overview.md
index f7804f14..38ce1ff6 100644
--- a/docs/nipoppy/overview.md
+++ b/docs/nipoppy/overview.md
@@ -1,3 +1,7 @@
+{%
+    include-markdown "nipoppy/cli_note.md"
+%}
+
 ## What is Nipoppy? 
 
 [Nipoppy](https://github.com/neurodatascience/nipoppy) is a lightweight framework for analyzing (neuro)imaging and clinical data. It is designed to help users do the following:
diff --git a/docs/nipoppy/trackers.md b/docs/nipoppy/trackers.md
index 1eba3cb7..059fa7fc 100644
--- a/docs/nipoppy/trackers.md
+++ b/docs/nipoppy/trackers.md
@@ -1,3 +1,7 @@
+{%
+    include-markdown "nipoppy/cli_note.md"
+%}
+
 ## Track data availability status
 
 ---
diff --git a/docs/nipoppy/workflow/bids_conv.md b/docs/nipoppy/workflow/bids_conv.md
index 1e959bca..8c4aa187 100644
--- a/docs/nipoppy/workflow/bids_conv.md
+++ b/docs/nipoppy/workflow/bids_conv.md
@@ -1,3 +1,7 @@
+{%
+    include-markdown "nipoppy/cli_note.md"
+%}
+
 ## Objective
 
 ---
diff --git a/docs/nipoppy/workflow/dicom_org.md b/docs/nipoppy/workflow/dicom_org.md
index b3f6d0e6..ba72e2dd 100644
--- a/docs/nipoppy/workflow/dicom_org.md
+++ b/docs/nipoppy/workflow/dicom_org.md
@@ -1,3 +1,7 @@
+{%
+    include-markdown "nipoppy/cli_note.md"
+%}
+
 ## Objective
 
 ---
diff --git a/docs/nipoppy/workflow/proc_pipe/fmriprep.md b/docs/nipoppy/workflow/proc_pipe/fmriprep.md
index f8cd07a5..fbe3b97c 100644
--- a/docs/nipoppy/workflow/proc_pipe/fmriprep.md
+++ b/docs/nipoppy/workflow/proc_pipe/fmriprep.md
@@ -1,3 +1,7 @@
+{%
+    include-markdown "nipoppy/cli_note.md"
+%}
+
 ## Objective
 
 ---
diff --git a/docs/nipoppy/workflow/proc_pipe/mriqc.md b/docs/nipoppy/workflow/proc_pipe/mriqc.md
index e394a9e6..1259f2fb 100644
--- a/docs/nipoppy/workflow/proc_pipe/mriqc.md
+++ b/docs/nipoppy/workflow/proc_pipe/mriqc.md
@@ -1,3 +1,7 @@
+{%
+    include-markdown "nipoppy/cli_note.md"
+%}
+
 ## MRIQC image processing pipeline
 
 ---