SummaryMinimal residual disease (MRD) is an important independent prognostic factor for relapse and survival in acute lymphoblastic leukaemia (ALL). Compared with adult B‐cell ALL, reports of adult T‐cell ALL (T‐ALL) MRD have been scarce and mostly based on molecular methods. We evaluated the prognostic value of multiparameter flow cytometry (FCM)‐based MRD at the end of induction (EOI‐MRD). The present retrospective study included 94 adult patients with T‐ALL. MRD was detected by six‐ to eight‐colour FCM. Patients who were EOI‐MRD positive had a higher cumulative incidence of relapse (CIR) (87·6% vs. 38·8%, P = 0·0020), and a lower relapse‐free survival (RFS) (5·4% vs. 61·0%, P = 0·0005) and overall survival (OS) (32·7% vs. 69·7%, P < 0·0001) than those who were EOI‐MRD negative. Moreover, for patients who received allogeneic haematopoietic stem cell transplantation (allo‐HSCT) at their first remission, EOI‐MRD positivity was predictive of post‐transplant relapse (2‐year CIR: 68·2% vs. 4·0%, P = 0·0003). Multivariate analysis showed that EOI‐MRD was an independent prognostic factor for CIR [hazard ratio (HR) 2·139, P = 0·046], RFS (HR 2·125, P = 0·048) and OS (HR 2·987, P = 0·017). In conclusion, EOI‐MRD based on FCM was an independent prognostic factor for relapse and survival in adult T‐ALL. For patients who underwent HSCT, EOI‐MRD could be used to identify patients with a high risk of relapse after allo‐HSCT.