When collecting oral and faecal samples for large epidemiological microbiome studies, optimal storage conditions such as immediate freezing, are not always feasible. It is fundamental to study the impact of temporary room temperature (RT) storage and shipping on the microbiome diversity obtained in different types of samples. We performed a pilot study aimed to validate the sampling protocol based on the viability of the 16S rRNA gene sequencing in microbiome samples. Faecal and oral samples from five participants were collected and preserved in different conditions: i) 70% ethanol; ii) in a FIT tube for stool samples; and iii) in a chlorhexidine solution for oral wash samples. Four aliquots were prepared per sample, which were stored at RT, and frozen at days 0, 5, 10 and 15, respectively.