MXenes have excellent properties as electrode materials in energy storage devices or fuel cells. In bioelectrochemical systems (for wastewater treatment and energy harvesting), MXenes can have antimicrobial characteristics in some conditions. Here, different intercalation and delamination approaches to obtain Ti3C2Tx MXene flakes with different terminal groups and lateral dimensions are comprehensively investigated. The effect of these properties on the energy harvesting performance from wastewater is then assessed. Regardless of the utilized intercalant molecules, MXene flakes obtained using soft delamination approaches are much larger (up to 10 µm) than those obtained using mechanical delamination methods (<1.5 nm), with a relatively higher content of ─O/─OH surface terminations. When employed in microbial fuel cells, electrodes made of these large MXene flakes have demonstrated a power density of over 400% higher than smaller MXene flakes, thanks to their lower charge transfer resistance (0.38 Ω). These findings highlight the crucial role of selecting appropriate intercalation and delamination methods when synthesizing MXenes for bioelectrochemical applications.