Meerkats are group-living, insectivorous herpestids in which subordinate members provide extensive care for the dominant female's young. In contrast to some cooperative breeders, subordinate female meerkats are physiologically able to reproduce and occasionally do so successfully; their attempts are more frequently ‘suppressed’ via eviction or infanticide by the dominant female. Spontaneous abortion and neonatal loss occur with some regularity, further negatively impacting reproductive success. Here, we compared the reproductive outcomes and endocrine profiles, including of serum progesterone (P4), serum estradiol (E2), and fecal glucocorticoid metabolites (fGCm), of dominant and subordinate dams residing within their clans in the Kalahari Desert of South Africa. Our study spanned years of drought, which reduced insect abundance and represented a substantial environmental stressor. Meerkat pregnancies were identified at mid-term and culminated either in spontaneous abortions or full-term deliveries, after which pups were either lost prior to emergence from the natal den (usually within 2 days of birth) or emerged at 2–3 weeks. Neonatal loss exceeded fetal loss for all females, and contributed to narrowing the status-related disparity in female reproductive output seen during less arid periods. Although E2 concentrations were significantly lower in subordinate than dominant females, they were sufficient to support gestation. Absolute E2 concentrations may owe to androgenic precursors that also attain highest concentrations in dominant dams and may mediate aggression underlying female reproductive skew. Pregnancies terminating in fetal loss were marked by significantly lower P4 concentrations in mid-gestation and modestly lower E2 concentrations overall. Consistently high fGCm concentrations further increased across trimesters, particularly (but not consistently) in subordinates and in aborted pregnancies. Environmental stressors may modulate reproductive outcomes in meerkats through their influence on sex steroids and their effects on intragroup competition. The social and eco-physiological factors affecting intraspecific variation in reproductive output, even in obligate cooperative breeders, may be most apparent during extreme conditions, reflecting the benefits of long-term studies for assessing the impact of climate change.