BACKGROUND: Reducing the burden of anaemia is a critical global health priority that could improve maternal outcomes amongst pregnant women and their neonates. As more counties in Kenya commit to universal health coverage, there is a growing need for optimal allocation of the limited resources to sustain the gains achieved with the devolution of healthcare services. This study aimed to describe the spatio-temporal patterns of maternal anaemia prevalence in Kenya from 2016 to 2019. METHODS: Quarterly reported sub-county level maternal anaemia cases from January 2016 - December 2019 were obtained from the Kenyan District Health Information System. A Bayesian hierarchical negative binomial spatio-temporal conditional autoregressive (CAR) model was used to estimate maternal anaemia prevalence by sub-county and quarter. Spatial and temporal correlations were considered by assuming a conditional autoregressive and a first-order autoregressive process on sub-county and seasonal specific random effects, respectively. RESULTS: The overall estimated number of pregnant women with anaemia increased by 90.1% (95% uncertainty interval [95% UI], 89.9-90.2) from 155,539 cases in 2016 to 295,642 cases 2019. Based on the WHO classification criteria, the proportion of sub-counties with normal prevalence decreased from 28.0% (95% UI, 25.4-30.7) in 2016 to 5.4% (95% UI, 4.1-6.7) in 2019, whereas moderate anaemia prevalence increased from 16.8% (95% UI, 14.7-19.1) in 2016 to 30.1% (95% UI, 27.5-32.8) in 2019 and severe anaemia prevalence increased from 7.0% (95% UI, 5.6-8.6) in 2016 to 16.6% (95% UI, 14.5-18.9) in 2019. Overall, 45.1% (95% UI: 45.0-45.2) of the estimated cases were in malaria-endemic sub-counties, with the coastal endemic zone having the highest proportion 72.8% (95% UI: 68.3-77.4) of sub-counties with severe prevalence. CONCLUSION: As the number of women of reproductive age continues to grow in Kenya, the use of routinely collected data for accurate mapping of poor maternal outcomes remains an integral component of a functional maternal health strategy. By unmasking the sub-county disparities often concealed by national and county estimates, our study findings reiterate the importance of maternal anaemia prevalence as a metric for estimating malaria burden and offers compelling policy implications for achieving national nutritional targets.