The forest habitat in this ecoregion is highly fragmented, and the remaining natural habitats are becoming even more fragmented as agriculture and other human activities are increasing.

The biodiversity values of the forests are recognized as being of global importance. Although the last decade has seen an increase in conservation efforts in this region, threats, problems and pressures still persist and are even increasing, including overexploitation of natural resources, lack of coordinated activities, lack of implementing and integrating policies, and a decline of fundamental resources for the responsible government sectors.

Areas between the forests have different characteristics depending on the country in question; in it is mainly farmland, in and it is generally savanna woodland/thicket with farmed areas increasing. The ecoregion also includes the larger offshore islands of Pemba, Zanzibar, Mafia and the Bazaruto Archipelago, as well as the smaller isles in the Indian Ocean close to the coast.

As the Eastern Africa Coastal Forests have long been isolated from other regions of tropical moist forests by expanses of drier savannas and grasslands, it has an exceptionally high level of plant endemism that has recently led to part of it being classified as the Swahili Centre of endemism. Elsewhere within the region (Somalia and Mozambique), studies at a few sites have also noted the occurrence of endemic trees, but overall the number of endemic species is thought to be greatly underestimated due to civil strife that has prevented further exploration.

At present it is estimated that there are 2 km2 in Somalia, 660 km2 in Kenya, 697 km2 in Tanzania, 16 km2 in Malawi, 3 km2 in Zimbabwe and more than perhaps more then 1790 km2 in Mozambique. Most forests are small (< 20 km2) and over 80% of the coastal forests are located on government land, mainly gazetted as forest reserves. Only 26.2 km2 in the region are designated as national parks: Arabuko-Sokoke (6.2 km2), ; Mlola forest on Mafia Island (20 km2), ; and tiny patches in .