Various jEdit and plugin windows can be docked into the view for convenience. Dockable windows have a popup button in their top-left corner. Clicking this button displays a menu with commands for docking the window in one of four sides of the view.

On each side of the text area where there are docked windows, a strip of buttons is shown. There is a button for activating each docked window, as well as a close box and a popup menu button, which when clicked shows a menu for moving or undocking the currently selected window. The popup menu also contains a command for opening a new floating instance of the current window.

The commands in the View>Docking menu move keyboard focus between docking areas.

Dockable windows can also be configured in the Docking pane of the Utilities>Global Options dialog box.