•Therapies for treatment-resistant depression need to be improved.•Lifestyle modification might be effective against treatment-resistant depression.•Insufficient patient recruitment probably prevented confirmation in this study.•Our program improved life quality and decreased use of antidepressants.•The COVID-19 pandemic made it difficult to perform more thorough evaluations. The high prevalence of depression is partly attributable to the poor response of patients to first-line antidepressants. Multimodal programs that promote a healthy lifestyle are successful in treating depression when used as a complementary therapy, but their medium- and long-term benefits have not been demonstrated for patients with treatment-resistant depression (TRD). The main aim of this study was to compare the effectiveness of a lifestyle modification program (LMP) with mindfulness-based cognitive therapy (MBCT) and a placebo-control (written suggestions for lifestyle changes) in Spanish patients with TRD. This controlled clinical trial randomized 94 patients with TRD into 3 arms. The primary outcome was the Beck Depression Inventory-II (BDI-II) score at baseline, 2, 6 and 12 months. The secondary outcomes were changes in scores that evaluated quality-of-life, adherence to the Mediterranean diet, physical activity, and social support. Relative to the placebo group, the LMP and MBCT groups had significantly better quality of life (p = 0.017; p = 0.027), and the LMP group had significantly better adherence to the Mediterranean diet (p<0.001) and reduced use of antidepressants (p = 0.036). However, the three groups showed no significant differences in BDI-II score. Only about half of the planned 180 patients were recruited, in part due to the COVID-19 pandemic. There was no evidence that the LMP treatment significantly reduced symptoms of depression relative to the other groups during the COVID-19 lockdown.