OBJECTIVE: In Brazil, national estimates of childhood malnutrition have not been updated since 2006. The use of health information systems is an important complementary data source for analysing time trends on health and nutrition. This study aimed to examine temporal trends and socio-demographic inequalities in the prevalence of malnutrition in children attending primary health care services between 2009 and 2017. DESIGN: Time trends study based on data from Brazil's Food and Nutrition Surveillance System. Malnutrition prevalence (stunting, wasting, overweight and double burden) was annually estimated by socio-demographic variables. Prais-Winsten regression models were used to analyse time trends. Annual percent change (APC) and 95 % CI were calculated. SETTING: Primary health care services, Brazil. PARTICIPANTS: Children under 5 years old. RESULTS: In total, 15,239,753 children were included. An increase in the prevalence of overweight (APC = 3·4 %; P = 0·015) and a decline in the prevalence of wasting (-6·2 %; P = 0·002) were observed. The prevalence of stunting (-3·2 %, P = 0·359) and double burden (-1·4 %, P = 0·630) had discrete and non-significant reductions. Despite the significant reduction in the prevalence of undernutrition among children in the most vulnerable subgroups (black, conditional cash transfer's recipients and residents of poorest and less developed areas), high prevalence of stunting and wasting persist alongside a disproportionate increase in the prevalence of overweight in these groups. CONCLUSIONS: The observed pattern in stunting (high and persistent prevalence) and increase in overweight elucidate setbacks in advances already observed in previous periods and stresses the need for social and political strategies to address multiple forms of malnutrition.