To study the differences in the prevalence, risk, and grade of control of different cardiometabolic comorbidities in patients with primary aldosteronism (PA) and essential hypertension (EH) matched by age, sex, and blood pressure levels at diagnosis. Case-control study of a secondary base (PA patients in follow-up in a tertiary hospital between 2018 and 2020). Controls were patients with non-functioning adrenal incidentalomas and EH, matched by age, sex, and baseline diastolic blood pressure (DBP) and systolic blood pressure (SBP). Fifty patients with PA and 50 controls were enrolled in the study. At diagnosis, PA patients had a higher prevalence of chronic kidney disease (CKD) than controls (18.4% vs. 2.1%, P = 0.008). No differences were detected in the prevalence of other cardiometabolic comorbidities nor in their degree of control (P > 0.05). All patients received antihypertensive medical treatment and 10 PA patients underwent unilateral laparoscopic adrenalectomy. After a median follow-up of 31.9 [IQR = 1.0-254.8] months, PA patients presented a greater degree of declination of kidney function than controls (average decrease in glomerular filtration rate (MDRD-4) -17.6 ± 3.1 vs. -2.8 ± 1.8 ml/min/1.73 m2, P < 0.001). There were no differences in the grade of SBP (P = 0.840) and DBP control (P = 0.191), nor in the risk of developing other comorbidities or in their degree of control. PA patients have a higher prevalence of CKD at the time of diagnosis when compared to EH matched by age, sex, and blood pressure levels. Furthermore, the risk of kidney function impairment throughout the follow-up is significantly greater in PA patients and is independent of the degree of blood pressure control.