In the drier areas heather dominates, interspersed with cross-leaved heath and purple moor grass. In the wetter areas purple moor grass forms characteristic dense tussocks. Common cottongrass and marsh cinquefoil occur in the wet mire conditions.

The range of habitats encourages a very rich variety of invertebrates for an area of only 6.5 hectares. There are many notable species, as well as over 200 different species of moth and 150 species of spider.

The ponds hold a number of water beetles and dragonflies are a common sight, darting around the ponds in summer. Species include four-spotted chaser, blue-tailed damselfly and locally occurring black darter.

Allerthorpe Common is a particularly good place to see adders and lizards. One of the best times to see adders is on warm days in February when they emerge from hibernation.

The reserve is at its best in early summer when the wavy hair-grass adds an atmospheric haze to the heather.