The use of additive manufacturing in metals by powder bed fusion via electron beam (PBF-EB) is increasing for fabricating high-quality parts meeting industrial standards. However, high surface roughness poses a consistent challenge in PBF-EB. This study investigates two novel approaches to optimise surface roughness for a given machine and powder combination. Using machine control software’s recently introduced research mode functionality, we develop customised beam control code to effectively explore a vast parameter space. Additionally, we explored the impact of beam travel direction and spot morphology on surface roughness. Line-melt-based contours were explored by specimen manufacturing with layer-wise parameter change, whilst spot-melting-based samples were built using a full factorial design of experiments with four factors at three levels. Initial sample characterisation was done using a stylus-based contact profilometer, followed by detailed evaluation using focus variation microscopy. Results reveal that increasing beam power and spot energy exacerbate surface roughness. We also find that a well-defined energy distribution at the spot's edge contributes to smoother surfaces. Whilst the influence of beam travel direction on surface roughness remains uncertain, our findings underscore the importance of parameter selection in achieving optimal results. By adjusting contouring parameters, we achieve a vertical roughness of Ra17.7 ± 0.9 (Sa 21.6), significantly lower than in the current literature. These findings advance our understanding of surface roughness optimisation in PBF-EB and offer practical insights for improving part quality in industrial applications. By harnessing tailored beam control strategies, manufacturers can enhance the capabilities of additive manufacturing technologies in producing metal components.