Modern lifestyle is associated with a major consumption of ultra-processed foods (UPF) due to their practicality and palatability. The ingestion of emulsifiers, a main additive in UPFs, has been related to gut inflammation, microbiota dysbiosis, adiposity and obesity. Maternal unbalanced nutritional habits during embryonic and perinatal stages perturb offspring’s long-term metabolic health, thus increasing obesity and associated comorbidity risk. However, whether maternal emulsifier consumption influences developmental programming in the offspring remains unknown. Here we show that, in mice, maternal consumption of dietary emulsifiers (1% CMC and 1% P80 in drinking water), during gestation and lactation, perturbs the development of hypothalamic energy balance regulation centers of the progeny, leads to metabolic impairments, cognition deficits and induces anxiety-like traits in a sex-specific manner. Our findings support the notion that maternal consumption of emulsifiers, common additives of UPFs, causes mild metabolic and neuropsychological malprogramming in the progeny. Our data call for nutritional advice during gestation. Overall design: Total RNA samples from P21 male mice (4 control litters and 5 emulsifiers litters) were processed at the IDIBAPS genomics’ platform for Tapestation quality control and subsequent sequencing. All samples had an RNA integrity number (RIN) > 8. mRNA strand-specific RNA libraries were generated using 200 ng of total RNA using the Stranded mRNA Prep Ligation kit (Illumina) following the manufacturer’s instructions. Libraries were sequenced on an Illumina NextSeq2000 (Illumina) in paired-end mode with a read length of 2×50 bp. Around 40 million of paired-end reads were generated for each sample/condition.