Despite the clearing of the land for livestock raising, the difficult access to many areas has made possible for sanctuaries of well-preserved forest to still exist, with trees such as the jacarandá, Spanish cedar, canjerana, guatambu, ipê, canela, angico, jequitibá, and also the araucaria, more typical of subtropical South America but found in the area because of altitude.

At its closest point, the region is only 100 km (62 mi) from the city of São Paulo.

It is also the habitat of a varied fauna: pampas deer (locally known as veado campeiro), maned wolves (lobo guará), cougars (onça-parda or suçuarana), bush dogs (cachorro-vinagre), ocelots (jaguatirica), pacas, howler monkeys (bugio), Atlantic titis (sauá), squirrels, and hedgehogs can still be found there.

Birds of note are the azure jay, the toucan, the scaly-headed parrot (maitaca), the inhambu, the jacana, the seriema and the crested caracara.

The Mantiqueira is a popular region for mountain climbers and trekkers, where in winter, which is the dry season, one can climb some of the highest peaks in the country: Here are also some of the highest Brazilian cities: Due to altitude, winter in the Serra da Mantiqueira sees low temperatures, with the occurrence of fog in early morning and frost, giving the landscape the appearance of regions with a much colder climate.