Rue has a culinary use, but since it is bitter and gastric discomfort may be experienced by some individuals, it is used sparingly. Although used more extensively in former times, it is not a herb that is typically found in modern cuisine. Today it is largely unknown to the general public and most chefs, and unavailable in grocery stores. It is a component of berbere, the characteristic Ethiopian spice mixture, and as such is encountered in Ethiopian cuisine. Also in Ethiopia, fresh rue is dipped in coffee before drinking it.

It was used extensively in ancient Near Eastern and Roman cuisine (according to Ibn Sayyar al-Warraq and Apicius).

Rue is used as a traditional flavouring in Greece and other Mediterranean countries.

In Istria (a region in Croatia), and in Northern Italy, it is used to give a special flavour to grappa/raki and most of the time a little branch of the plant can be found in the bottle. This is called grappa alla ruta.

Seeds can be used for porridge.

The bitter leaf can be added to eggs, cheese, fish, or mixed with damson plums and wine to produce a meat sauce.

In Italy in Friuli Venezia-Giulia, the young branches of the plant are dipped in a batter, deep-fried in oil, and consumed with salt or sugar. They are also used on their own to aromatise a specific type of omelette.

Used in Old World beers as flavouring ingredient.