Based on @FranBurstall, I looked at the documentation, and then I wrote the following:

```lisp
;; Define a function to enable markdown-mode after Emacs Anywhere is invoked
(defun pmd/markdown-mode-emacs-anywhere (app-name window-title x y w h)
 (markdown-mode))

;; Hook your function
(add-hook 'ea-popup-hook 'pmd/markdown-mode-emacs-anywhere)
```

Not sure if this is the most elegant way to do it... But it works! :)

I tried removing all parameters. But it broke the function. So I am leaving it with all this *unused* parameters.