Aim: Early assessment of patient preferences has the potential to support shared decisions in personalized precision medicine for patients with rheumatoid arthritis (RA). The aim of this study was to assess treatment preferences of patients with RA (< 5 years) with previous experience of inadequate response to first-line monotherapy. Method: Patients were recruited (March–June 2021) via four clinics in Sweden. Potential respondents (N = 933) received an invitation to answer a digital survey. The survey included an introductory part, a discrete choice experiment (DCE) and demographic questions. Each respondent answered 11 hypothetical choice questions as part of the DCE. Patient preferences and preference heterogeneity were estimated using random parameter logit models and latent class analysis models. Results: Patients (n = 182) assessed the most important treatment attributes out of physical functional capacity, psychosocial functional capacity, frequency of mild side effects and likelihood of severe side effects. In general, patients preferred a greater increase in functional capacity and decreased side effects. However, a substantial preference heterogeneity was identified with two underlying preference patterns. The most important attribute in the first pattern was the ‘likelihood of getting a severe side effect’. Physical functional capacity was the most important attribute in the second pattern. Conclusion: Respondents focused their decision-making mainly on increasing their physical functional capacity or decreasing the likelihood of getting a severe side effect. These results are highly relevant from a clinical perspective to strengthen communication in shared decision making by assessing patients’ individual preferences for benefits and risks in treatment discussions.