BACKGROUND: We describe a clinic-randomized trial to improve chronic kidney disease (CKD) care through a CKD-clinical decision support (CKD-CDS) intervention in primary care clinics and the challenges we encountered due to COVID-19 care disruption. METHODS/DESIGN: Primary care clinics (N = 32) were randomized to usual care (UC) or to CKD-CDS. Between April 17, 2019 and March 14, 2020, more than 7000 patients had accrued for analysis by meeting study-eligibility criteria at an index office visit: age 18-75, laboratory criteria for stage 3 or 4 CKD (eGFR 15-59 mL/min/1.73 m(2)), and one or more opportunities algorithmically identified to improve CKD care such as blood pressure (BP) or glucose control, angiotensin converting enzyme inhibitor (ACEI) or angiotensin receptor blocker (ARB) use, discontinuance of a nonsteroidal anti-inflammatory drug (NSAID), or nephrology referral. At CKD-CDS clinics, CDS provided individualized treatment suggestions that were printed for patients and clinicians at the start of office encounters and were viewable within the electronic health record. By initial design, the impact of the CKD-CDS intervention on care gaps was to be assessed 12 months after the index date, but COVID-19 caused major disruptions to care delivery during the intervention period. In response to disruptions, the intervention was temporarily suspended while we expanded CDS use for telehealth encounters and programmed new criteria for displaying the CKD-CDS to intervention patients due to clinic closures and scheduling changes. DISCUSSION: We describe a NIH-funded pragmatic trial of web-based EHR-integrated CKD-CDS and modifications necessary mid-study to complete the study as intended in the face of COVID-19 pandemic challenges.