The Hajj is an annual pilgrimage to Mecca and one of the largest gathering of people in the world. Most Indonesian pilgrims are senior adults and elderly adults, who are more prone to acquire infections during the Hajj ritual. The aims of this study are to investigate the dynamics of Streptococcus pneumoniae colonization and to investigate antibiotic susceptibility of pneumococcal strains in Indonesian pilgrims. This was a prospective multi-site longitudinal study in Indonesian hajj pilgrims aged >18 years old in the year 2015. Nasopharyngeal swabs were collected from the same subject before departure and upon arrival at the airport. S. pneumoniae was identified using conventional and molecular approach, while antibiotic susceptibility was determined using a disk diffusion method. Among 813 Hajj pilgrims who were enrolled from five sites in this study, the prevalence of S. pneumoniae carriage rates before- and after-the Hajj were 8.6% (95% CI 6.7–10.5%) and 8.2% (95% CI 6.4–10.1%), (p value: 0.844) respectively. Serotype 16F, 6A/6B, 3, 18, and 23F were the five most prevalent serotypes before Hajj, whereas serotypes 3, 34, 13, 4, and 23F were the most prevalent serotypes after Hajj. Serotype 3 was identified as most acquired serotype during Hajj in Indonesian pilgrim. There was an increase in the percentage of isolates susceptible to co-trimoxazole after Hajj (42.9% versus 57.4%). The study provided an overview of the change of dynamics of S. pneumoniae serotype acquisition in Indonesian Hajj Pilgrims. Along with data of vaccination serotypes coverage and antimicrobial susceptibility, these findings may contribute to recommendation of vaccination and treatment policies in the future.