This study evaluated Clostridium autoethanogenum protein (CAP) as an alternative to soybean meal (SBM) in rainbow trout (Oncorhynchus mykiss) diets and examined the potential confounding influence of microcrystalline cellulose (MCC) used as a filler. In the in vitro digestibility assay, six treatments ranging from 0 % to 25 % CAP (in 5 % increments) were tested, with MCC as an inert filler to maintain a similar nutrient composition. In vivo, rainbow trout (initial weight ~ 84 g) were fed diets with CAP replacing 0 % (Control), 50 % (CAPS6), and 100 % (CAPS12) of SBM for 67 days. In vitro results indicated that adding MCC to CAP-containing diets had a nutrient-dilution effect and reduced digestibility. Thereafter, in vivo results for feed intake (FI), feed conversion ratio (FCR), and the digestibility of dry matter (DM) and gross energy (GE) were corrected. The corrected results showed no significant differences in FI and FCR among treatments, whereas digestibility of DM and GE was reduced in CAPS12. Uncorrected in vivo measurements showed that CAP-containing diets had comparable growth performance to the control group, whereas protein digestibility decreased in both CAPS6 and CAPS12, lipid digestibility declined significantly only in CAPS12, and phosphorus digestibility was significantly higher only in CAPS6. Solid nitrogen emissions increased in CAP diets, while dissolved nitrogen and both solid and dissolved phosphorus emissions were unaffected. Overall, CAP could be a viable alternative to SBM in rainbow trout diets. However, the use of fibrous fillers should be approached with caution in diets where high-protein ingredients replace conventional protein sources.