The COVID-19 pandemic that began in 2020 has significantly impacted businesses, regardless of size or industry. The hybrid and remote working models have moved all meetings with potential and existing suppliers to an online environment. This also applies to small- and medium-sized enterprises (SMEs), which have had to adapt themselves to the new situation and implement the solutions necessary to survive on the market. On the other hand, clients have become more aware of the environment and its changes. Customers are trying to be more eco-friendly, by choosing and moving towards Green IT. Thus, this needs to be considered. The acquisition of management information systems (MIS) in the pandemic era is based only on virtual meetings. The main goals of this paper were the identification of the changes in the negotiations caused by the COVID-19 pandemic, the transformation of this process into virtual environment, discussion of the possibility of using Green IT in addition to Management Information Systems, and the changes caused by the pandemic. The article was prepared based on the results of qualitative research using the case study method. The comparative analysis includes purposely selected cloud-based Enterprise Resource Planning (ERP) and Customer Relationship Management (CRM) systems’ acquisition processes, presented from the clients’ perspective. The research was conducted in 2021, based on the authors’ practical experience, and presents four cases. This research illustrates the negotiations concerning an acquisition transaction pre-pandemic and during the pandemic. Finally, the conclusions and main differences caused by the pandemic in the acquisition transaction process of management information systems (MIS) are presented.