Studying functional decline in multimorbidity patients is important for improving patient management. We sought to analyse long-term functional decline, mortality and institutionalization and associated factors in over-65-year-olds with multimorbidity, comparing with previous short-term results. A prospective study was conducted in three primary care centres, over 18months, in a random sample of patients (n = 241) ≥ 65years on a clinical care programme for multimorbidity. Primary outcomes were decrease in functional status category (Barthel or Lawton scales), alone and together with death and institutionalization. Other variables were sociodemographic characteristics, comorbidity, medications and hospitalisation. Patients initially included had five chronic conditions (IQR 4-6) and were on 11 (IQR 9-14) chronic medications; their median age was 82years (75th percentile 86); 38.2% had impaired function at baseline. Of the 216 patients included in the analysis, 47 died; 11 were institutionalized; and 158 completed follow-up, but of these, 81 (51.3%, 95% CI 43.5-58.9) experienced functional decline. That is, 139/216 (64.4%, 95% CI 57.8-70.4%) had outcome events and these were associated with older age (OR 1.1, 95% CI 1.0-1.1, p = 0.002) and having ≥ 1 admission during follow-up (OR 4.1, 95% CI 2.1-8.9%, p < 0.001). Considering all 241 patients, there were 234 admissions during follow-up, in 117 patients. Two-thirds of patients showed functional decline, died or were institutionalized. The factors associated with loss of function at 18months were similar to those observed at 8months, notably previous hospital admissions. These findings are important as they indicate functional decline and increasing care needs are potentially predictable/modifiable.