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Introduction Follow‐up after allogeneic transplantation in acute myeloid leukaemia (AML) is guided by measurable residual disease (MRD) testing. Quantitative polymerase chain reaction (qPCR) is the preferred MRD platform but unfortunately, 40%–60% of AML patients have no high‐quality qPCR target. This study aimed to improve MRD testing by utilising droplet digital PCR (ddPCR). ddPCR offers patient‐specific monitoring but concerns of tracking clonal haematopoiesis rather than malignant cells prompt further validation. Methods Retrospectively, we performed MRD testing on blood and bone marrow samples from AML patients transplanted by reduced‐intensity conditioning. Results The applicability of ddPCR was 39/42 (92.9%). Forty‐five ddPCR assays were validated with a 0.0089% median sensitivity. qPCR targeting NPM1 mutation detected relapse 46 days before ddPCR ( p = .03). ddPCR detected relapse 34.5 days before qPCR targeting WT1 overexpression ( p = .03). In non‐relapsing patients, zero false positive ddPCR MRD relapses were observed even when monitoring targets associated with clonal haematopoiesis such as DNMT3A , TET2 , and ASXL1 mutations. Conclusion These results confirm that qPCR targeting NPM1 mutations or fusion transcripts are superior in MRD testing. In the absence of such targets, ddPCR is a promising alternative demonstrating (a) high applicability, (b) high sensitivity, and (c) zero false positive MRD relapses in non‐relapsing patients.