Background: Understorey plants are key to maintaining forest structure and functioning. They protect the soil, improve its structure and fertility, reduce water run-off and sustain the below-ground biota, amongst other ecological services. However, little is known about the environmental conditions that regulate the occurrence of these plants. This study focuses on determining how canopy cover influences the occurrence of understorey species and identifying the most important soil properties that affect these species. The study area was a pine-oak forest in the Sierra Madre Occidental, an important source of ecological services for northwestern Mexico. Methods: To assess the conditions influencing the presence of herbaceous and shrub species, 25 soil variables were examined in relation to the species occurring in forest gaps and under the canopy. Sampling was conducted in five plots, each of 100 × 100 m. In each plot, 4 subplots, each of 20 × 20 m, were each subdivided in a grid of 2 × 2 m units, in which the presence-absence of herbaceous and shrub species was recorded (2000 units in total). Soil samples were extracted for analysis from the central point in each subplot. Data were analyzed using a Binomial Logistic Model (BLM) and Random Forest (RF) classification. Results: Understorey species were more strongly affected by soil variables than by their location in gaps or below canopy. The concentrations of Ca, P, K, Fe, Na, C, Zn, Mn, nitrates, organic matter, sand, silt, and percentage water saturation were statistically significantly associated with the presence of some plant species, whilst no significant differences were found in regard to preference for gaps or canopy, although several species were more frequent in open areas. Conclusions: Given the importance of the understorey cover in forest system functioning, we propose that understorey should be considered in integrated management and conservation practices for the temperate forests of northern Mexico.