Abstract Background Management of patients with polypharmacy is challenging, and evidence for beneficial effects of deprescribing interventions is mixed. This study aimed to investigate whether a patient-centred deprescribing intervention of PCPs results in a reduction of polypharmacy, without increasing the number of adverse disease events and reducing the quality of life, among their older multimorbid patients. Methods This is a cluster-randomised clinical study among 46 primary care physicians (PCPs) with a 12 months follow-up. We randomised PCPs into an intervention and a control group. They recruited 128 and 206 patients if ≥60 years and taking ≥five drugs for ≥6 months. The intervention consisted of a 2-h training of PCPs, encouraging the use of a validated deprescribing-algorithm including shared-decision-making, in comparison to usual care. The primary outcome was the mean difference in the number of drugs per patient (dpp) between baseline and after 12 months. Additional outcomes focused on patient safety and quality of life (QoL) measures. Results Three hundred thirty-four patients, mean [SD] age of 76.2 [8.5] years participated. The mean difference in the number of dpp between baseline and after 12 months was 0.379 in the intervention group (8.02 and 7.64; p = 0.059) and 0.374 in the control group (8.05 and 7.68; p = 0.065). The between-group comparison showed no significant difference at all time points, except for immediately after the intervention (p = 0.002). There were no significant differences concerning patient safety nor QoL measures. Conclusion Our straight-forward and patient-centred deprescribing procedure is effective immediately after the intervention, but not after 6 and 12 months. Further research needs to determine the optimal interval of repeated deprescribing interventions for a sustainable effect on polypharmacy at mid- and long-term. Integrating SDM in the deprescribing process is a key factor for success. Trial registration Current Controlled Trials, prospectively registered ISRCTN16560559 Date assigned 31/10/2014. The Prevention of Polypharmacy in Primary Care Patients Trial (4P-RCT).