In this work sulfided CoMo/MgAl2O4 catalysts used in fluid bed catalytic hydropyrolysis for the conversion of biomass to liquid fuels were thoroughly characterized by Raman spectroscopy and scanning (transmission) electron microscopy together with energy dispersive X-ray spectroscopy. Potassium and calcium were transferred from the biomass to the catalyst and the accumulated amounts increased proportionally with the time on stream (TOS) and reached 0.67 and 0.28 wt.% after 16.2 h, respectively, when beech wood was used as biomass feedstock with a feeding rate of approximately 270 g/h beech wood to 50 g of catalyst. The carbon content on the spent catalyst also increased with TOS and was 3.7 wt.% after 3.5 h and 7.2 wt.% after 16.2 h, indicating that the coking rate decreased with time on stream. However, SEM-EDS indicated that the carbon concentration increased more on the surface than in the bulk, thereby increasing the risk of pore blocking. In addition, Raman spectroscopy showed that the initially formed coke was mostly graphitic, but the coke became less ordered as successive layers grew on top. Doping the catalyst with K2CO3, corresponding to a potassium loading of 1.9 wt.%, prior to the sulfidation, led to a higher degree of stacking and increased the slab length of the MoS2 particles. Furthermore, SEM images of the spent catalyst indicated that the catalyst particles were encapsulated by a layer of coke during pyrolysis, but this layer was continuously removed by knock-off. This indicates that potassium acts as a catalyst for polymerization of tar and coking reactions on the catalyst. The effect of using wheat straw, which contains 10 times more potassium than beech wood, as feedstock was also investigated. This led to defluidization due to agglomeration within the first 0.3 h on stream. SEM images showed that agglomerates of char and catalyst particles, with a diameter up to 5 mm, were formed due to polymerization of the metaplast and tar. Additionally, SEM-EDS images showed that potassium was well-distributed in the agglomerates, indicating that potassium catalyzed the formation of these agglomerates.