To strengthen the coordinating function of general practitioners (GPs) in the German healthcare system, a copayment of €10 was introduced in 2004. Due to a perceived lack of efficacy and a high administrative burden, it was abolished in 2012. The present cohort study investigates characteristics and differences of GP-coordinated and uncoordinated patients in Bavaria, Germany, concerning morbidity and ambulatory specialist costs and whether these differences have changed after the abolition of the copayment. We performed a retrospective routine data analysis, using claims data of the Bavarian Association of the Statutory Health Insurance Physicians during the period 2011–2012 (with copayment) and 2013–2016 (without copayment), covering 24 quarters. Coordinated care was defined as specialist contact only with referral. Multinomial regression modelling, including inverse probability of treatment weighting, was used for the cohort analysis of 500 000 randomly selected patients. Longitudinal regression models were calculated for cost estimation. Coordination of care decreased substantially after the abolition of the copayment, accompanied by increasing proportions of patients with chronic and mental diseases in the uncoordinated group, and a corresponding decrease in the coordinated group. In the presence of the copayment, uncoordinated patients had €21.78 higher specialist costs than coordinated patients, increasing to €24.94 after its abolition. The results indicate that patients incur higher healthcare costs for specialist ambulatory care when their care is uncoordinated. This effect slightly increased after abolition of the copayment. Beyond that, the abolition of the copayment led to a substantial reduction in primary care coordination, particularly affecting vulnerable patients. Therefore, coordination of care in the ambulatory setting should be strengthened.