Until the early 1990s, short-sea shipping (SSS) was widely regarded as a forgotten component within the European transportation system, with freight transportation within Europe dominated by unimodal transportation means, notably road vehicles. Since then, however, with changes in circumstance, SSS has experienced a change in fortune, with the EU intended to alter the sector's image from being slow, worn-out and poor quality to being efficient, high quality and competitive which can lead to a substantial modal shift from unimodal road vehicles, as well as forming an integral part of an integrated multimodal logistical supply chain within Europe complementing the objectives of trans- European transport network characterized by cohesion, integration and intermodality. In this sense, nodal efficiency i.e. port becomes a critical component in deciding whether such ambitious objectives can be achieved, especially given the existence of serious bottlenecks in many European ports as identified by the EC, e.g. worn-out port infra- and superstructure, non-flexible working hours, lack of IT adapted to SSS, congestion, complicated power relation within ports and poor hinterland connections, etc. Nevertheless, throughout the years, it is interesting, and indeed surprising, to found that the introduction of port security, which is likely to pose significant implications on port efficiency and thus SSS's competitiveness, remains a largely untouched topic, as reflected by the EC approach which largely regards port security and SSS as completely independent and unrelated projects. Recognizing such deficiency, this chapter aims to address this gap by investigating the potential implications of port security measures on the competitiveness of European SSS and providing a critical review on the current EC approach on the issue, as well as discussing the challenges ahead. By rekindling their overlapping relation, it is anticipated that this chapter will play a contributory role in the development of multimodal freight transportation in Europe.