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<b><i>Introduction:</i></b> Preventing or delaying frailty has important benefits. Studies show the effectiveness of multifactorial interventions in the frail and pre-frail elderly, but few have evaluated their long-term effectiveness. Frailty and its consequences have been shown to increase the use of health resources. The main aim was to evaluate the long-term effect of a multifactorial primary healthcare intervention in pre-frail elderly people at 36 months and determine the health resources used and their cost. <b><i>Methods:</i></b> A follow-up of a cohort study of patients who participated in a randomized clinical trial in an urban primary care centre in Barcelona was carried out. We included 200 non-institutionalized people aged ≥80 years who met the Fried pre-frailty criteria. The intervention group (IG) received a 6-month interdisciplinary intervention based on physical exercise, Mediterranean diet advice, assessment of inadequate prescribing in polypharmacy patients, and social assessment, while the control group (CG) received standard of care primary healthcare treatment. Sociodemographic variables were collected at baseline. The Fried criteria, comorbidities, and geriatric syndromes were collected at baseline and 12 and 36 months. For the analysis of health costs, data were collected on visits, complementary tests, hospital admissions, and surgical interventions in the last 36 months. Complexity, the rate of expected emergency admission, and the rate of expected mortality were collected at 36 months. Between-group characteristics were compared at baseline and 36 months using the χ² test and the <i>t</i> test for independent samples. The post-intervention (12-month follow-up) versus longitudinal follow-up (36-month follow-up) comparison used McNemar’s test for each group. The nonparametric Mann-Whitney test was used to compare health costs. <b><i>Results:</i></b> Of the 200 patients initially included, we evaluated 135 (67.5%) patients who completed the 36-month follow-up. The mean age was 88.5 years and 64.4% were female. At 36 months, the transition to frailty was much lower in the IG than in the CG (22.1% vs. 32.8%, <i>p</i> = 0.013). The total mean health cost at 36 months was 3,110 EUR in the CG and 2,679 EUR in the IG. No significant between-group differences were observed according to Clinical Risk Groups. <b><i>Conclusions:</i></b> A multifactorial, interdisciplinary intervention carried out in primary care prevented frailty in pre-frail elderly people at 36-month follow-up. Although the IG was grouped into higher grade Clinical Risk Groups and therefore had greater morbidity, the cost was lower than that in the CG.