Background: Current evidence for the effectiveness of post-stroke cognitive rehabilitation is weak, possibly due to two reasons. First, patients typically express cognitive deficits in several domains. Therapies focusing on specific cognitive deficits might not address their interrelated neurological nature. Second, co-occurring psychological problems are often neglected or not diagnosed, although post-stroke depression is common and related to cognitive deficits. This pilot trial aims to test a rehabilitation program in virtual reality that trains various cognitive domains in conjunction, by adapting to the patient's disability and while investigating the influence of comorbidities. Methods: Thirty community-dwelling stroke patients at the chronic stage and suffering from cognitive impairment performed 30 min of daily training for 6 weeks. The experimental group followed, so called, adaptive conjunctive cognitive training (ACCT) using RGS, whereas the control group solved standard cognitive tasks at home for an equivalent amount of time. A comprehensive test battery covering executive function, spatial awareness, attention, and memory as well as independence, depression, and motor impairment was applied at baseline, at 6 weeks and 18weeks follow-up. Results: At baseline, 75% of our sample had an impairment in more than one cognitive domain. The experimental group showed improvements in attention (χ 2 F (2) = 9.57, p < .01), spatial awareness (χ 2 F (2) = 11.23, p < .01) and generalized cognitive functioning (χ 2 F (2) = 15.5, p < .001). No significant change was seen in the executive function and memory domain. For the control group, no significant change over time was found. Further, they worsened in their depression level after treatment (T = 45, r = .72, p < .01) but returned to baseline at follow-up. The experimental group displayed a lower level of depression than the control group after treatment (Ws = 81.5, z = − 2.76, r = − .60, p < .01) and (Ws = 92, z = − 2.03, r = − .44, p < .05). Conclusions: ACCT positively influences attention and spatial awareness, as well as depressive mood in chronic stroke patients. Trial registration: The trial was registered prospectively at ClinicalTrials.gov (NCT02816008) on June 21, 2016.