In this study, optimization of solid-state fermentation of Camelina sativa residues (camelina straw, CS) and Panicum virgatum (switchgrass, SG) by Trametes versicolor 52J (TV52J), Trametes versicolor m4D (TVm4D), and Phanerochaete chrysosporium (PC) was conducted. At optimal conditions, the tensile strength, unit density and mass loss for CS pellets were 6.2 MPa, 1139 kg m−3, and 33%, respectively after 31 d pretreatment by TVm4D, while for SG pellets, they were 1.6 MPa, 1244 kg m−3 , and 13.8%, respectively after 32 d pretreatment by TVm4D. Although the holocellulose content of microbially pretreated CS and SG pellets dropped from 58.6 to 36.7%, and from 66.2 to 46.3%, respectively, the glucose yield of CS pellets increased from 12.9 to 61.1% with a corresponding xylose yield increase from 14.7 to 60.1%. The glucose and xylose yield of SG increased from 10.9 to 59.9% and 13.4 to 35.7%, respectively. It can be concluded that microbial pretreatment contributed to mass loss of the samples but trivially affected the energy content and significantly boosted the physical properties and enzymatic digestibility of the treated pellets. The microbially pretreated CS is recommended for densification and combustion while the microbially pretreated SG is more suitable for biochemical conversion.