Mammillaria karwinskiana subs. nejapensis grows in tropical deciduous forest and xerophyllous scrub. It is quite common, but it is threatened by deforestation for small-holder agriculture and goat-ranching.
Mammillaria karwinskiana subs. nejapensis (Mammillaria nejapensis) is very variable, especially for the length of the spines, and at the beginning there were two recognized varieties: var. brevispina (short spined form) and var. longispina (long spined form), with respectively short and long spines, but they are merely local or individual variations. This species branches basally or more frequently forms large colonies by dichotomous division.