BACKGROUND: We explored the associations of comorbidities with cognitive deterioration, institutionalization, and mortality in biomarker-confirmed Alzheimer's disease (AD) dementia. METHODS: We conducted a Swedish Register-based cohort study consisting of 10,857 people (mean age 74 years) with diagnosed dementia and positive AD biomarkers (CSF Abeta(42)/P-tau(181) ratio). Cognitive function was measured by mini-mental state examination (MMSE). Comorbidities by human body organ systems (e.g., diseases of the circulatory system) and six selected comorbidities: type-2 diabetes (T2DM), ischemic heart disease (IHD), stroke, chronic kidney disease (CKD), inflammatory bowel disease, and depression, were analyzed. Multistate Cox regressions assessed the associations of comorbidities with cognitive deterioration, institutionalization, and death. RESULTS: Only T2DM and IHD were associated with cognitive deterioration. Mental disorders, T2DM, and stroke were linked to higher hazards of institutionalization. Endocrine-metabolic disorders, circulatory system diseases, and CKD were associated with higher mortality rates. CONCLUSIONS: Comorbidities may help inform the prognosis of biomarker-confirmed AD dementia. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13195-025-01807-6.