The rocky cliffs of the area are sparsely wooded with Burkea africana, Detarium microcarpum, Lannea acida, Sterculia setigera and Combretum ghasalense.

On the deep soils of some of the summits and the Atakora escarpment, there is a greater variety of plant species with Isoberlinia doka and Afzelia africana.

The park includes both the Sudanian and Guinean savannas, with areas of grassland dominated by Acacia sieberiana and Mitragyna inermis or Terminalia macroptera.

Pendjari National Park has a relatively large population of elephants, which was stable over the last decades and counted more than 800 individuals between 2005 and 2010.

[3] One of the rarest large predators in the protected area is the Northwest African cheetah (Acinonyx jubatus hecki).

The African fish eagle (Haliaeetus vocifer) and Pel's fishing-owl (Scotopelia peli) can also be found.

Among the more notable species recorded are pied-winged swallow (Hirundo leucosoma), white-crowned robin-chat (Cossypha albicapillus), Botta's wheatear (Oenanthe bottae), familiar chat (Cercomela familiaris), white-fronted black-chat (Myrmecocichla albifrons), mocking cliff-chat (Thamnolaea cinnamomeiventris), common rock thrush (Monticola saxitilis), Senegal eremomela (Eremomela pusilla), blackcap babbler (Turdoides reinwardtii), red-winged pytilia (Pytilia phoenicoptera), black-rumped waxbill (Estrilda troglodytes), bush petronia (Petronia dentata) and Togo paradise-whydah (Vidua togoensis).