Background Heart failure (HF), type 2 diabetes (T2D) and chronic kidney disease (CKD) commonly coexist. We studied characteristics, prognosis and healthcare utilisation of individuals with two of these conditions. Methods We performed a retrospective, population-based linked electronic health records study from 1998 to 2020 in England to identify individuals diagnosed with two of: HF, T2D or CKD. We described cohort characteristics at time of second diagnosis and estimated risk of developing the third condition and mortality using Kaplan-Meier and Cox regression models. We also estimated rates of healthcare utilisation in primary care and hospital settings in follow-up. Findings We identified cohorts of 64 226 with CKD and HF, 82 431 with CKD and T2D, and 13 872 with HF and T2D. Compared with CKD and T2D, those with CKD and HF and HF and T2D had more severe risk factor profile. At 5 years, incidence of the third condition and all-cause mortality occurred in 37% (95% CI: 35.9%, 38.1%%) and 31.3% (30.4%, 32.3%) in HF+T2D, 8.7% (8.4%, 9.0%) and 51.6% (51.1%, 52.1%) in HF+CKD, and 6.8% (6.6%, 7.0%) and 17.9% (17.6%, 18.2%) in CKD+T2D, respectively. In each of the three multimorbid groups, the order of the first two diagnoses was also associated with prognosis. In multivariable analyses, we identified risk factors for developing the third condition and mortality, such as age, sex, medical history and the order of disease diagnosis. Inpatient and outpatient healthcare utilisation rates were highest in CKD and HF, and lowest in CKD and T2D. Interpretation HF, CKD and T2D carry significant mortality and healthcare burden in combination. Compared with other disease pairs, individuals with CKD and HF had the most severe risk factor profile, prognosis and healthcare utilisation. Service planning, policy and prevention must take into account and monitor data across conditions.