Abstract Study question To evaluate whether preimplantation genetic testing for aneuploidy (PGT-A) can improve pregnancy and neonatal outcomes for patients with limited good-quality embryos. Summary answer PGT-A failed to improve cumulative live birth rate or shorten time to pregnancy, but optimized pregnancy outcomes per transfer for patients with limited good-quality embryos. What is known already PGT-A is currently widely used to screen for aneuploidy with the goal of improving live birth rates. Remarkably, previous studies have focused on the effect of PGT-A on cumulative clinical outcomes in women with good pregnancy prognosis. However, it is still unclear whether PGT-A can improve the cumulative pregnancy outcomes in patients with limited good-quality embryos. Study design, size, duration A retrospective cohort study was performed among 1553 women who intended PGT-A for the first time but obtained only two or less good-quality embryos on day 3 after oocyte retrieval from March 2017 to June 2021. Participants/materials, setting, methods A total of 1553 patients were divided into two groups: 997 in the PGT-A group and 556 in the drop-out group of withdrawing PGT-A due to poor embryological outcome. Multivariable logistic regression was performed to adjust for potential confounders when comparing the clinical outcomes between two groups. Main results and the role of chance After adjusting for potential confounding factors, PGT-A group exhibited significantly lower cumulative rates of biochemical pregnancy (19.96% vs. 30.22%, P-adj < 0.001), clinical pregnancy (17.55% vs. 23.38%, P-adj < 0.001) and live birth (14.14% vs. 16.19%, P-adj = 0.005) per oocyte retrieval and longer median time to pregnancy and live birth compared with drop-out group. However, significant increases in rates of biochemical pregnancy (72.16% vs. 35.50%, P-adj < 0.001), clinical pregnancy (61.86% vs. 26.98%, P-adj < 0.001), and live birth (48.45 vs. 18.26%, P-adj < 0.001) per transfer were found in the PGT-A group. No significant differences were observed in cumulative miscarriage and ectopic pregnancy rates, number of ETs needed per live birth and neonatal outcomes. Limitations, reasons for caution This study was limited by the inherent potential bias of retrospective studies and small sample size. Thus, additional studies with larger sample sizes are needed to confirm our findings. Wider implications of the findings PGT-A failed to improve cumulative live birth rate or shorten time to pregnancy, but optimized pregnancy outcomes per transfer for patients with limited good-quality embryos. Trial registration number Not applicable