The article presents a processed dataset from amplicon sequencing of the V4 region of the 16S rRNA gene to recover bacterial and archaeal taxa from the caeca of multiple chicken breeds of Pakistan. These include chicken breeds commonly raised at commercial level, Naked Neck, Black Australorp, Rhode Island Red, White Layer, and Broiler. All the breeds were challenged with Newcastle Disease Virus (NDV), with vaccination against the disease also explored. This resulted in samples belonging to four treatment groups as: Control; Vaccinated; Vaccinated and Challenged; and Non-vaccinated and Challenged. These were raised on an antibiotic free diet in a semi-controlled farming setup. 16S rRNA gene amplicon sequencing of caecal DNA from day old and mature chicken samples (22 weeks for Naked Neck, Black Australorp, Rhode Island Red and White Layer; 8 weeks for Broiler) of the four groups was performed. The paired-end reads from all the samples were quality trimmed, error corrected, and overlapped, on which unique Operational Taxonomic Units (OTUs) were obtained at 99 % similarity. Using predictive modelling, the MetaCyc functional pathways, as well as KEGG orthologs were also recovered. The generated data may be used to explore microbial interactions in gastrointestinal tract with respect to NDV vaccination and infection, together with increased understanding of chicken health and productivity.