The prenatal period is a critical developmental juncture with enduring effects on offspring health trajectories. An individual's gut microbiome is associated with health and developmental outcomes across the lifespan. Prenatal stress can disrupt an infant's microbiome, thereby increasing susceptibility to adverse outcomes. This cross‐species systematic review investigates whether maternal prenatal stress affects the offspring's gut microbiome. The study analyzes 19 empirical, peer‐reviewed research articles, including humans, rodents, and non‐human primates, that included prenatal stress as a primary independent variable and offspring gut microbiome characteristics as an outcome variable. Prenatal stress appeared to correlate with differences in beta diversity and specific microbial taxa, but not alpha diversity. Prenatal stress is positively correlated with Proteobacteria, Bacteroidaceae, Lachnospiraceae, Prevotellaceae, Bacteroides, and Serratia. Negative correlations were observed for Actinobacteria, Enterobacteriaceae, Streptococcaceae, Bifidobacteria, Eggerthella, Parabacteroides, and Streptococcus. Evidence for the direction of association between prenatal stress and Lactobacillus was mixed. The synthesis of findings was limited by differences in study design, operationalization and timing of prenatal stress, timing of infant microbiome sampling, and microbiome analysis methods.