The seeds are large and form part of the diet of the Mexican jay and Abert's squirrel.

Pinus cembroides is a small to medium-size tree, reaching 8 to 20 metres (26 to 66 ft) tall and with a trunk diameter of up to 50 centimetres (20 in).

Many of the other pinyon pines have been treated as varieties or subspecies of it at one time or another in the past, but research in the last 10–50 years has shown that most are distinct species.

Mexican pinyon is a relatively non-variable species, with constant morphology over the entire range except for the disjunct population in the Sierra de la Laguna pine-oak forests of Baja California Sur; this is generally treated as a subspecies, Pinus cembroides subsp.

There is also a disjunct population in the Sierra de la Laguna of southern Baja California Sur.

It occurs at moderate altitudes, mostly from 1,600 to 2,400 m (5,200 to 7,900 ft), which some authorities consider a separate species (P. lagunae).