Graphene, a material composed of a two-dimensional lattice of carbon atoms, has due to its many unique properties a wide array of potential applications in the biomedical field. One of the most common production methods is exfoliation through sonication, which is simple but has low yields. Another approach, using microfluidization, has shown promise through its scalability for commercial production. Regardless of their production method, materials made for biomedical applications need to be tested for biocompatibility. Here, we investigated the differences in toxicity, macrophage response, and complement activation of similar-sized graphene flakes produced through sonication and microfluidization, using in vitro cell assays and in vivo assays on zebrafish larvae. In vitro toxicity testing showed that sonicated graphene had a high toxicity, with an EC50 of 100 μg mL-1 for endothelial cells and 60 μg mL-1 for carcinoma cells. In contrast, microfluidized graphene did not reach EC50 at any of the tested concentrations. The potency to activate the complement system in whole blood was 10-fold higher for sonicated than for microfluidized graphene. In zebrafish larvae, graphene of either production method was found to mainly agglomerate in the caudal hematopoietic tissue; however, no acute toxic effects were found. Sonicated graphene led to an increase in macrophage count and a macrophage migration to the ventral tail area, while microfluidized graphene led to a transient reduction in macrophage count and fewer cells in the ventral trail area. The observed reduction in macrophages and change in macrophage distribution following exposure to microfluidized graphene was less pronounced compared to sonicated graphene and contributed to masking of the fluorescent signal rather than cytotoxic effects. Summarized, we observed higher toxicity, macrophage response, and complement activation with graphene produced through sonication, which could be due to oxygen-containing functional groups introduced to the edge of the carbon lattice by this production method. These findings indicate that microfluidization produces graphene more suitable for biomedical applications.