Introduction: The objective of this study was to evaluate quality indicators of secondary health care in chronic kidney disease (CKD).Methods: This retrospective longitudinal study was conducted in an outpatient medical nephrology clinic of the Brazilian Unified Health System (UHS) and a multidisciplinary outpatient clinic of a private health plan (PHP). The inclusion criteria were age ≥ 18 years, ≥ 3 medical appointments, and follow‐up time ≥ 6 months.Results: Compared to PHP patients (n = 183), UHS patients (n = 276) were older (63.4 vs. 59.7 years, p = 0.04), had more arterial hypertension (AH) (91.7% vs. 84.7%, p = 0.02) and dyslipidemia (58.3 vs. 38.3%, p < 0.01), and had a lower estimated baseline glomerular filtration rate (eGFR) (29.9 [21.5–42.0] vs. 39.1 [28.6–54.8] mL/min/1.73 m2, p < 0.01). Compared to PHP patients, UHS patients had a lower percentage of diabetics with glycated hemoglobin < 7.5% (46.1% vs. 61.2%, p = 0.03), fewer people with potassium < 5.5 mEq/L (90.4% vs. 95.6%, p = 0.04), and fewer referrals for hemodialysis with functioning arteriovenous fistula (AVF) (9.1% vs. 54.3%, p < 0.01). The percentages of people with hypertension and blood pressure < 140 × 90 mmHg were similar between the UHS and PHP groups (59.7% vs. 66.7%; p = 0.17), as was the percentage of people with parathyroid hormone control (85.6% vs. 84.8%; p = 0.83), dyslipidemia and LDL‐cholesterol < 100 mg/dL (38.3% vs. 49.3%; p = 0.13), phosphorus < 4.5 mg/dL (78.5% vs. 72.0%; p = 0.16), and 25‐OH‐vitamin‐D > 30 ng/mL (28.4% vs. 36.5%; p = 0.11). The crude reduction in eGFR was greater in the UHS group than in PHP (2.3 [−0.1; 5.9] vs. 1.1 [−1.9; 4.6] mL/min/1.73 m2; p < 0.01). In the multivariate linear mixed‐effects model, UHS patients also showed faster CKD progression over time than PHS ones (group effect, p < 0.01; time effect, p < 0.01; interaction, p < 0.01).Conclusions: Quality of care for patients with CKD can be improved through both services, and multidisciplinary care may have a positive impact on the control of comorbidities, the progression of CKD, and the planning of the initiation of hemodialysis.