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Objective To estimate the effectiveness of a Medication Discrepancy Detection Service (MDDS), a collaborative service between the community pharmacy and Primary Care. Design Non-controlled before-and-after study. Setting Bidasoa Integrated Healthcare Organisation, Gipuzkoa, Spain. Participants The service was provided by a multidisciplinary group of community pharmacists (CPs), general practitioners (GPs), and primary care pharmacists, to patients with discrepancies between their active medical charts and medicines that they were actually taking. Outcomes The primary outcomes were the number of medicines, the type of discrepancy, and GPs’ decisions. Secondary outcomes were time spent by CPs, emergency department (ED) visits, hospital admissions, and costs. Results The MDDS was provided to 143 patients, and GPs resolved discrepancies for 126 patients. CPs identified 259 discrepancies, among which the main one was patients not taking medicines listed on their active medical charts (66.7%, n = 152). The main GPs’ decision was to withdraw the treatment (54.8%, n = 125), which meant that the number of medicines per patient was reduced by 0.92 (9.12 ± 3.82 vs. 8.20 ± 3.81; p < .0001). The number of ED visits and hospital admissions per patient were reduced by 0.10 (0.61 ± .13 vs 0.52 ± 0.91; p = .405 and 0.17 (0.33 ± 0.66 vs. 0.16 ± 0.42; p = .007), respectively. The cost per patient was reduced by €444.9 (€1003.3 ± 2165.3 vs. €558.4 ± 1273.0; p = .018). Conclusion The MDDS resulted in a reduction in the number of medicines per patients and number of hospital admissions, and the service was associated with affordable, cost-effective ratios.