A three year pneumococcal carriage study was set up in Belgium when the vaccination programme switched from a 13-valent (PCV13) to a 10-valent (PCV10) vaccine. We compared the first follow-up period (October 2016 - June 2017, year 2, Y2) for nasopharyngeal carriage, serotype distribution and antimicrobial susceptibility of S. pneumoniae with the baseline (January-July 2016, year 1, Y1). A single nasopharyngeal swab was taken in children (6-30 months), either attending one of the 112 day-care centres (DCCs), or visiting one of the 21 physicians for an acute otitis media (AOM). S. pneumoniae were cultured, screened for antimicrobial susceptibility, and serotyped. In Y2, 1218 samples were collected. The majority of the Y2-children (>85%) was vaccinated appropriately for their age. Children in Y2 received either PCV13 only (DCC: 23.5%; AOM: 24.6%), PCV10 only (DCC: 29.8%; AOM: 37.7%), or a mix of both vaccines (DCC: 31.9%; AOM: 25.4%). Pneumococcal carriage rates were high (Y2, DCC: 68.2%; AOM: 64.8%). Among carriers, prevalence of PCV13 serotypes was low (Y2 vs Y1, DCC: 3.5% vs 5.4%; AOM: 7.6% vs 7.7%). Although prevalence of PCV13-non-PCV10 serotypes did not increase significantly compared to Y1 (Y2 vs Y1, DCC: 1.6% vs 0.9%; Y2 vs Y1, AOM: 5.1% vs 0.0%), the proportion of serotypes 3, 6A, 19A among PCV13 serotype carriers in DCC was significantly higher in Y2 (46.2% vs Y1: 16.0%, p-value = 0.034). Serotypes 23B and 15B were the predominant non-vaccine serotypes (Y2). Among detected strains, non-susceptibility to at least one of five antibiotics tested (penicillin, tetracycline, erythromycin, levofloxacin, cotrimoxazole) was comparable to Y1 (Y2 vs Y1, DCC: 41.3% vs 42.4%; AOM: 49.4% vs 48.1%). After completion of the PCV13-to-PCV10 vaccine switch in Belgium, the proportion of PCV13-non-PCV10 serotypes (mainly 19A) significantly increased among PCV13 serotype carriers in DCC, stressing the need for strengthened surveillance as the PCV10-vaccinated population grows. Copyright © 2019 Elsevier Ltd. All rights reserved.