Background: Improving diet quality in chronic kidney disease (CKD) is challenging due to a myriad of competing recommendations. Patient-centered goal setting can facilitate dietary behavior change; however, its role in improving diet quality in CKD has not been investigated. Aim: The aim of the study is to evaluate the effects of goal setting on improving diet quality in stages 3–4 CKD. Methods: Forty-one participants completed a 6-month dietitian-led telehealth (combined coaching calls and text messages) intervention as part of a larger RCT. Participants set one to two diet-related SMART goals and received weekly goal tracking text messages. Dietary intake was assessed using the Australian Eating Survey at baseline, 3, and 6 months, with diet quality determined using the Alternate Healthy Eating Index (AHEI). Results: Significant improvements in AHEI (+6.9 points; 95% CI 1.2–12.7), vegetable (+1.1 serves; 95% CI 0.0–2.3) and fiber intake (+4.2 g; 95% CI 0.2–8.2) were observed at 3 months in participants setting a fruit and/or vegetable goal, compared with those who did not. However, no significant or meaningful changes were observed at 6 months. No other goal setting strategy appeared in effect on diet intake behavior or clinical outcomes in this group of CKD participants. Conclusions: Patient-centered goal setting, particularly in relation to fruit and vegetable intake, as part of a telehealth coaching program, significantly improved diet quality (AHEI), vegetable and fiber intake over 3 months. More support may be required to achieve longer-term behavior change in stages 3–4 CKD patients.