Objective This study aimed to provide population-level data regarding trends in multimorbidity over 13 years. Methods We linked provincial health administrative data in Ontario, Canada, to create 3 cross-sectional panels of residents of any age in 2003, 2009, and 2016 to describe: (i) 13-year trends in multimorbidity prevalence and constellations among residents and across age, sex, and income; and (ii) chronic condition clusters. Multimorbidity was defined as having at least any 2 of 18 selected conditions, and further grouped into levels of 2, 3, 4, or 5 or more conditions. Age-sex standardized multimorbidity prevalence was estimated using the 2009 population as the standard. Clustering was defined using the observed combinations of conditions within levels of multimorbidity. Results Standardized prevalence of multimorbidity increased over time (26.5%, 28.8%, and 30.0% across sequential panels), across sex, age, and area-based income. Females, older adults and those living in lower income areas exhibited higher rates in all years. However, multimorbidity increased relatively more among males, younger adults, and those with 4 or 5 or more conditions. We observed numerous and increasing diversity in disease clusters, namely at higher levels of multimorbidity. Conclusion Our study provides relevant and needed population-based information on the growing burden of multimorbidity, and related socio-demographic risk factors. Multimorbidity is markedly increasing among younger age cohorts. Also, there is an increasing complexity and lack of common clustering patterns at higher multimorbidity levels. Supplementary Information The online version contains supplementary material available at 10.17269/s41997-021-00474-y.