diff --git a/concepts/activation.mdx b/concepts/activation.mdx
index b4f3eb6..ac00e35 100644
--- a/concepts/activation.mdx
+++ b/concepts/activation.mdx
@@ -247,8 +247,8 @@ sequenceDiagram
     rect rgb(235, 248, 240)
       Note over P: bash
       P->>P: run setup scripts
-      P->>P: set user variables
       P->>P: source profile.d scripts (plugins)
+      P->>P: set user variables
       P->>P: source hook.on-activate
       P->>P: exec FLOX_SHELL
     end
@@ -278,10 +278,13 @@ which is also the variable you can use to override which shell Flox uses when
 you activate an environment.
 
 As part of this activation script,
-Flox runs some initial setup, then sets the variables you've provided in the
-[[vars] section of your manifest](/man/manifest.toml#vars).
-It then sources every installed package's `profile.d` scripts — this is how
-[plugins](/concepts/plugins) hook into activation.
+Flox runs some initial setup, then sources every installed package's
+`profile.d` scripts — this is how [plugins](/concepts/plugins) hook into
+activation. This only happens in `dev` (the default) and `build` modes;
+`run` mode deliberately skips package `profile.d` scripts. Next, it sets
+the variables you've provided in the
+[[vars] section of your manifest](/man/manifest.toml#vars) — these aren't
+visible to profile.d scripts, only to what runs after them.
 Next, the script _sources_ the `hook.on-activate` script that you've provided
 in the [[hook] section of your manifest](/man/manifest.toml#hook).
 Since this script is run by the Bash shell we're using,