Pebble plains are a unique edaphic environment known only from the high valleys of the San Bernardino Mountains, California. The pebble plains have long been celebrated for the high vascular plant diversity they support, including at least six taxa endemic to the San Bernardino Mountains. Past research has shown that pebble plains soils differ most notably from nearby non-pebble plains soils in terms of their high clay content and loose, stony structure, especially in their upper-most horizon and on the soil surface. The stony upper horizon is probably the result of frost-heaving and erosion of soil particles by wind; the resulting accumulation of stone fragments at the soil surface is what inspired the name “pebble plains.” The combined effects of a friable, rocky surface, heavy lower horizons, frost heaving, high solar insolation, and desiccating winds are thought to limit recruitment of shrubs and trees and foster the persistence of a unique pebble plains flora consisting of herbaceous annuals and low-growing perennials. Despite decades of research involving the pebble plains and their unique flora, the soil chemical properties of pebble plains versus surrounding (non-pebble plains) soils has not been thoroughly investigated. This study investigates the chemistry of pebble plains soils to determine if they are chemically divergent from adjacent non-pebble plains soils. To answer this question, we collected soils from nine pebble plains areas, sampling from both the pebble plains themselves and from surrounding, non-pebble plain forests or shrublands. These samples were subjected to analyses for 13 soil chemical properties. Multivariate analyses of these data indicate that habitat type (pebble plains versus non-pebble plains) is the single most important factor explaining the variation in soil chemical properties. Although only Zn concentration is significantly divergent between the habitat types, pebble plains soils are generally deficient in major- and micronutrients compared to adjacent non-pebble plains soils. Our results suggest that while physical factors such as frost heave may be the primary agents responsible for the original formation and persistence of the pebble plains flora, the soils of the pebble plains are chemically unique, which may reinforce physical constraints on floristic composition in these areas.