Deforestation
The most severe threat facing cloud forests is deforestation. In the past, land has been cleared primarily for agricultural purposes, although development of housing/businesses could become an increasingly important factor in the future. The soil of cloud forests is generally quite fertile, but the topsoil layer is thin and is subject to rapid erosion once the forest is cleared because of the steep terrain. Decreasing soil quality causes farmers to resort to fertilizer and pesticide use, which creates a larger environmental problem because the cloud forest is often at the top of the watershed. A unique problem in some areas is that development to support the ecotourism industry has actually caused some additional damage to the forests themselves, or to other ecosystems and habitats that lie just beneath the edges of the cloud forests (where houses or farms are likely to be built.)

Hunting and poaching
While the Monteverde Cloud Forest Preserve is well patrolled against poachers, cloud forests in other parts of Central America continue to face serious threats from hunting. Several large mammals, including jaguars, pumas, and tapirs, were extirpated from the Monteverde area prior to the formation of the Preserve. Large birds such as guans and tinamous are also especially vulnerable to hunting pressures, and populations of these birds in the Monteverde Preserve are still recovering from prior lows caused by hunting. In other parts of the world the poaching continues.

Global Climate Change
A less obvious and more difficult problem to solve is the potential disruptive effect of global climate change. The scientific community is now fairly certain that global warming is a real phenomenon. Cloud forests are especially vulnerable because they rely on a combination of geographical and environmental factors that produce the misty and moist environment. Increasing temperatures would cause cloud lines to move farther up the mountain, reducing the area of cloud forests. In Monteverde, where the cloud forest exists in a band only 300-400m in elevation, upward movement of the cloud line by even 50-100m would have a large impact. Local biologists have already noted that bird and bat species seem to be expanding their ranges upward, while amphibians that used to reside at the top of the mountain have disappeared altogether.

Increasing UV exposure
The thinning of the stratospheric ozone layer allows more ultraviolet light through the atmosphere. This may be especially damaging in mountain areas where UV exposure is already higher. Potential impact to biological communities is poorly understood, although higher UV levels are hypothesized to be involved in global amphibian population declines. Like global warming, destruction of the ozone layer is a global problem that requires worldwide cooperation to solve.

Exotic species
As is the case throughout the world, exotic (non-native) species may pose a threat to cloud forest ecosystems. There are already dozens of exotic plants in the Monteverde area, although none seems to be causing substantial disruption yet. A foreign pest could potentially cause epidemics similar to the chestnut and elm blights of the United States. This type of threat is extremely difficult to guard against, especially in Central American countries that lack the funding to address management of problem organisms once they begin to become established.