Geoffroea decorticans is a drought-tolerant native tree of the Atacama Desert, one of the most extreme hyper-arid environments on Earth. Despite its ecological and socioeconomic value, little is known about its genetic status across a fragmented distribution. This study aimed to characterize the genetic diversity and population structure, and to assess evidence of genetic bottlenecks to propose conservation strategies for long-term persistence. We genotyped 194 individuals from eight natural populations spanning the species' range in northern Chile using nine nuclear microsatellite loci. We analyzed genetic diversity, differentiation, and structure. In addition, bottleneck signatures were evaluated through heterozygosity excess, allele frequency distribution, and M-ratio tests, and the effective population size (Ne) was estimated for each population. Null-allele frequencies were low across the studied loci. Most populations exhibited moderate to high levels of genetic diversity (Ar = 3.86, H_O = 0.73, H_E = 0.625) and significant heterozygote excess (F_IS = −0.192). Pairwise linkage disequilibrium patterns across loci varied among populations, and we detected significant genetic structure and differentiation. Multiple populations showed evidence of recent and/or historical bottleneck events, with low effective population sizes (N_E-LD < 20). We documented genetic variation, population structure, and bottleneck signals in G. decorticans populations across the Atacama Desert and emphasized the urgency of genetic monitoring. Conservation plans should prioritize populations based on genetic information, including those with low diversity, strong bottleneck signals, and high uniqueness; promote rigorous evaluation of source materials for future assisted gene flow programs, and protect habitat corridors to maintain adaptive potential under increasing aridification.