E-commerce is always more diffused as a selling channel around the whole world market, and its importance has increased and continues to increase with the COVID-19 pandemic emergency. It provides enterprises a lot of opportunities, as the importance of physical stores to sell goods is bypassed. However, it has also changed the role of logistics in the supply chain. For this reason, this work aims to identify the main logistics research areas related to e-commerce implementation and the factors and key performance indicators, which should be taken into account for each logistics research area, with particular attention to sustainable aspects. For doing this, a structured and comprehensive literature analysis is carried out. Keywords associated with e-commerce and logistics areas are matched to identify the most interesting works related to its implementation. From the analysis, five main research areas are identified: Supply Chain Network Design (SCND); Outbound Logistics (OL); Reverse Logistics (RL); Warehousing (WR); and IT and data management (E-IT). For each area, key factors, strategies and performance indicators have been identified. Finally, a methodological framework that summarizes the results of the analysis is presented; this is a useful tool for managers to implement or expand their e-commerce business. Many works are focused on one research area, carrying out critical factors, models, and methods to implement that topic. Instead, the methodological framework presented here summarizes multiple research areas from a logistic point of view, identifying for each one input and output variables and how they influence each other.