Organophosphate flame retardants (OPFRs) are used in a variety of products such as clear coats, resins, and plastics; however, research into their toxicological effects is limited. p-Tert-butylphenyl diphenyl phosphate (BPDP) and isopropylphenyl phosphate (IPPP) are two OPFRs that were prioritized for whole-animal toxicological studies based on observed effects in cultured avian hepatocytes in a previous study. The present study investigates the toxicity of BPDP and IPPP in chicken embryos at different developmental stages by evaluating morphological and gene expression endpoints. Chicken eggs were exposed via air cell injection to 0-250 μg/g (nominal) of either compound and then artificially incubated. At day 11 (midincubation), liver samples were collected for mRNA expression analysis; and at day 20 (1 day prehatch), morphological measurements and liver samples for transcriptomic evaluation were collected. At 250 μg/g, gallbladder size was significantly reduced for both compounds, head/bill length and tarsus length were significantly decreased, and liver somatic index was significantly increased following IPPP exposure only. No effects on mortality were observed up to the highest administered concentration for either chemical. Using a ToxChip polymerase chain reaction array, we report significant differences in hepatic gene expression for both compounds and time points; the most pronounced transcriptomic effects occurred at midincubation. Genes related to xenobiotic metabolism, bile acid/cholesterol regulation, and oxidative stress were significantly dysregulated. Given these changes observed throughout avian embryonic development, further research into the long-term effects of BPDP and IPPP are warranted, especially as they pertain to liver cholestasis. Environ Toxicol Chem 2022;41:739-747. © 2021 Her Majesty the Queen in Right of Canada. Environmental Toxicology and Chemistry © 2021 SETAC. Reproduced with the permission of the Minister of Environment and Climate Change Canada.