Multicentric B cell lymphoma (mBCL) is a common canine neoplasm with highly variable outcome. Hypervariable lymphocyte antigen receptor genes can serve as markers to monitor minimal residual disease (MRD) using next-generation sequencing (NGS). This study aimed to determine 1) if MRD assessment by NGS (MRD-NGS) for canine mBCL can predict time to relapse or overall survival, 2) the best sampling time points during and after treatment, and 3) whether the peripheral blood mononuclear cells (PBMCs) or the plasma fraction of blood is more sensitive for the detection of MRD. Antigen receptor genes were sequenced from lymph node samples of 36 dogs and MRD-NGS from blood was completed for 10 of these. In seven of eight patients that achieved complete clinical remission, molecular relapse was identified before clinical relapse. The neoplastic clone was identified more frequently in plasma than PBMCs. Additional samples need to be assessed to substantiate these results.