Background Chronic kidney disease (CKD) is a highly prevalent disease worldwide. A basic pillar for the management of a patient with CKD is the safe use of drugs. Inadequate dosing of medication or contraindicated drugs in renal impairment can lead to negative outcomes. The primary objective was to analyse the drug prescriptions of patients with CKD from two primary care centres to see if they were optimally adapted to the patient's estimated glomerular filtration rate (eGFR). Methods A retrospective observational study was conducted in two urban primary care centres. The study period was between September–October 2019. Patients over 18 years of age, with established CKD and with an eGFR less than 60 mL/min/1.73m2 for at least three months were included. Their demographic data (age and sex) and clinical variables such as associated comorbidities, eGFR value were retrospectively registered. Finally, their medication plans were reviewed in order to detect: inappropriate prescribing (IP), defined as an incorrect dose/frequency or contraindicated drug according to the renal function of the patient; nephrotoxic drugs and drugs with a high sodium content. Results A total of 273 patients were included. The most common patient profile was an elderly woman, polymedicated, with other concomitant diseases and with mild CKD. Two hundred and one IPs were detected, 13.9% of which were contraindicated drugs. Of all patients, 49.1% had been prescribed at least one IP on their medication plan, 93.8% had some potentially nephrotoxic drug and 8.4% had drugs with a high sodium content prescribed. Conclusions Patients with CKD are at increased risk of medication-related problems. It is necessary to implement measures to improve the safety in the prescription of drugs in patients with CKD.