Objective The quality of physician–patient interaction can have a significant impact on medication adherence. Little is known about this relationship in patients with lupus nephritis. Methods A cross-sectional, quantitative study. Data collected included demographics, current medication, systemic lupus erythematosus disease activity index, medication adherence, beliefs about medicines, shared decision-making, patient–doctor depth of relationship, patient–doctor quality of relationship, interpersonal trust in a physician and illness perceptions. Results Ninety-eight patients with lupus nephritis completed the questionnaires. Logistic regression indicated that medication adherence was significantly predicted by (a) interpersonal trust in a physician (B = 0.85, Wald 3.94, 95% confidence interval (CI) 1.01, 5.44; P = 0.05); (b) timeline cyclical (B = –0.89, Wald 4.95, 95% CI 0.19, 0.90; P < 0.05) and beliefs about the necessity of medicines (B = 0.75, Wald 4.14, 95% CI 1.03, 4.38; P < 0.05). Mediation analysis showed that beliefs about the necessity of medicines significantly mediated the relationship between trust and medication adherence when adjusted for age (B = 0.48, 95% CI 0.06, 1.08; P < 0.01). A further mediation analysis showed that patient–doctor depth of relationship (B = 0.05, 95% CI 0.01, 0.09; P < 0.001), shared decision-making (B = 0.07, 95% CI 0.01, 0.13; P < 0.001) and patient–doctor quality of relationship (B = 0.08, 95% CI 0.01, 0.16; P < 0.001) significantly mediated the relationship between illness coherence and interpersonal trust in a physician. Conclusion The findings highlighted two key elements: (a) the importance of trust in relation to medication adherence; and (b) a good understanding of patients’ illness is linked to a better relationship with their doctor and greater participation in shared decision-making which is associated with increased trust. Tailored psycho-educational interventions could contribute to improving the patient–doctor relationship quality, trust and increased shared decision-making, which, in turn, might improve medication adherence in patients with lupus nephritis.