diff --git a/docs/nipoppy/cli_note.md b/docs/nipoppy/cli_note.md
new file mode 100644
index 00000000..93965316
--- /dev/null
+++ b/docs/nipoppy/cli_note.md
@@ -0,0 +1,9 @@
+!!! note
+
+    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 [nipoppy.readthedocs.io](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/overview.md b/docs/nipoppy/overview.md
index f7804f14..93c0fb2a 100644
--- a/docs/nipoppy/overview.md
+++ b/docs/nipoppy/overview.md
@@ -1,3 +1,7 @@
+{%
+    include-markdown "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: