Late Quaternary histories of two North American desert biomes—C₄ grasslands and C₃ shrublands—are poorly known despite their sensitivity and potential value in reconstructing summer rains and winter temperatures. Plant macrofossil assemblages from packrat midden series in the northern Chihuahuan Desert show that C₄ grasses and annuals typical of desert grassland persisted near their present northern limits throughout the last glacial-interglacial cycle. By contrast, key C₃ desert shrubs appeared somewhat abruptly after 5000cal.yrBP. Bioclimatic envelopes for select C₄ and C₃ species are mapped to interpret the glacial-interglacial persistence of desert grassland and the mid-to-late Holocene expansion of desert shrublands. The envelopes suggest relatively warm Pleistocene temperatures with moist summers allowed for persistence of C₄ grasses, whereas winters were probably too cold (or too wet) for C₃ desert shrubs. Contrary to climate model results, core processes associated with the North American Monsoon and moisture transport to the northern Chihuahuan Desert remained intact throughout the last glacial-interglacial cycle. Mid-latitude effects, however, truncated midsummer (July-August) moisture transport north of 35° N. The sudden expansion of desert shrublands after 5000cal.yrBP may be a threshold response to warmer winters associated with increasing boreal winter insolation, and enhanced El Niño-Southern Oscillation variability.