To push gate performance to levels beyond the thresholds for quantum error correction, it is important to characterize the error sources occurring on quantum gates. However, the characterization of non-Markovian error poses a challenge to current quantum process tomography techniques. Fast Bayesian Tomography (FBT) is a self-consistent gate set tomography protocol that can be bootstrapped from earlier characterization knowledge and be updated in real-time with arbitrary gate sequences. Here we demonstrate how FBT allows for the characterization of key non-Markovian error processes. We introduce two experimental protocols for FBT to diagnose the non-Markovian behavior of two-qubit systems on silicon quantum dots. To increase the efficiency and scalability of the experiment-analysis loop, we develop an online FBT software stack. To reduce experiment cost and analysis time, we also introduce a native readout method and warm boot strategy. Our results demonstrate that FBT is a useful tool for probing non-Markovian errors that can be detrimental to the ultimate realization of fault-tolerant operation on quantum computing.