BackgroundSince 2014, Belgium’s Superior Health Council has recommended pneumococcal vaccination for adults aged 19–85 years at increased risk for pneumococcal diseases with a specific vaccine administration sequence and timing. Currently, Belgium has no publicly funded adult pneumococcal vaccination program. This study investigated the seasonal pneumococcal vaccination trends, evolution of vaccination coverage and adherence to the 2014 recommendations.MethodsINTEGO is a general practice morbidity registry in Flanders (Belgium) that represents 102 general practice centres and comprised over 300.000 patients in 2021. A repeated cross-sectional study was performed for the period between 2017 and 2021. Using adjusted odds ratios computed via multiple logistic regression, the association between an individual’s characteristics (gender, age, comorbidities, influenza vaccination status and socioeconomic status) and schedule-adherent pneumococcal vaccination status was assessed.ResultsPneumococcal vaccination coincided with seasonal flu vaccination. The vaccination coverage in the population at risk decreased from 21% in 2017 to 18.2% in 2018 and then started to increase to 23.6% in 2021. Coverage in 2021 was highest for high-risk adults (33.8%) followed by 50- to 85-year-olds with comorbidities (25.5%) and healthy 65- to 85-year-olds (18.7%). In 2021, 56.3% of the high-risk adults, 74.6% of the 50+ with comorbidities persons, and 74% of the 65+ healthy persons had an adherent vaccination schedule. Persons with a lower socioeconomic status had an adjusted odds ratio of 0.92 (95% Confidence Interval (CI) 0.87–0.97) for primary vaccination, 0.67 (95% CI 0.60–0.75) for adherence to the recommended second vaccination if the 13-valent pneumococcal conjugate vaccine was administered first and 0.86 (95% CI 0.76–0.97) if the 23-valent pneumococcal polysaccharide vaccine was administered first.ConclusionPneumococcal vaccine coverage is slowly increasing in Flanders, displaying seasonal peaks in sync with influenza vaccination campaigns. However, with less than one-fourth of the target population vaccinated, less than 60% high-risk and approximately 74% of 50 + with comorbidities and 65+ healthy persons with an adherent schedule, there is still much room for improvement. Furthermore, adults with poor socioeconomic status had lower odds of primary vaccination and schedule adherence, demonstrating the need for a publicly funded program in Belgium to ensure equitable access.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12889-023-15939-7.