It has an area of just and is a crumbling flat-topped limestone plateau surrounded by 60 metre high cliffs. The only known permanent structure on it was a chapel built inside a cave in 1343, which was destroyed by an earthquake in 1856 that also sank part of the island. Until 1971 the Royal Navy and Royal Air Force used the island for target practice. It became a bird reserve in 1980. The Filfla Natural Reserve Act, enacted in 1988, provided for further restrictions on access and use, including a prohibition on fishing within a nautical mile (1.9 km) around due to the possibility of unexploded ordnance. Three species of sea birds breed on the islet: the European Storm Petrel (c.5,000 pairs), Cory's Shearwater (c.200 pairs) and Yellow-legged Gull (c.130pairs). A type of wall lizard (Podarcis filfolensis ssp. filfolensis) and door snail (Lampedusa imitatrix gattoi) are endemic to Filfla. A large wild leek, growing up to 2 m high, also occurs. There is a small rocky islet next to Filfla, called Filfoletta.
Access to Filfla is only possible for educational or scientific purposes and visitors must get prior permission from the Ministry responsible for the environment.
On the Maltese coast opposite Filfla are the archeological sites of Hagar Qim and Mnajdra, the Hamrija Tower (one of 13 watchtowers that Martin de Redin built around the coast of Malta), and a memorial to Walter Norris Congreve, one of Malta's British governors-general.