Electron beam melting-powder bed fusion (EBM-PBF) is an additive manufacturing process, which is able to produce parts in layer-by-layer fashion from a 3D model data. Currently application of this technology in parts manufacturing with high geometrical complexity has acquired growing interest in industry. To recommend the EBM process into industry for manufacturing parts, improved mechanical properties of final part must be obtained. Such properties highly depend on individual single melted track and single layer. In EBM, interactions between the electron beam, powder, and solid underlying layer affect the geometrical (e.g., re-melt depth, track width, contact angle, and track height) and microstructural (e.g., grain structure, and primary dendrite arm spacing) characteristics of the melted tracks. The core of the present research was to explore the influence of linear energy input parameters in terms of beam scanning speed, beam current as well as focus offset and their interactions on the geometry and microstructure of EBM-manufactured single tracks of Alloy 718. Increased scanning speed led to lower linear energy input values (<0.9 J/mm) in an specific range of the focus offset (0–10 mA) which resulted in instability, and discontinuity of the single tracks as well as balling effect. Decreasing the scanning speed and increasing the beam current resulted in higher melt pool depth and width. By statistical evaluations, the most influencing parameters on the geometrical features were primarily the scanning speed, and secondly the beam current. Primary dendrite arm spacing (PDAS) slightly decreased by increasing the scanning speed using lower beam current values as the linear energy input decreased. By increasing the linear energy input, the chance of more equiaxed grain formation was high, however, at lower linear energy input, mainly columnar grains were observed. The lower focus offset values resulted in more uniform grains along the 〈001〉 crystallographic direction.