Invasion of alien species is recognized as one of the most pressing global challenges altering the composition, structure and functioning of invaded ecosystems as well as the services they generated before the invasion. We consider the case of Norway maple (Acer platanoides) which was intentionally introduced to North America as an ornamental street shade tree, but now has been viewed as a serious threat to native forest ecosystems in the United States and Canada. Decisions about the management of invasive cases are inherently difficult because of the multifactorial and multiattribute scope of the problem. To facilitate management efforts, decision-makers and environmental practitioners require a software tool integrating relevant knowledge and acting as a supporting expert. The underlying methodology, conceptual design of the tool and its main modules are discussed in the paper. In particular, we argue for an approach taking into account the entire ecosystem purview of the problem, phases of invasion process, tree development stages and driving mechanisms underlying the cases of biological invasion. Functional architecture of a software tool for environmental modelling and decision-making in managing of invasive cases (EMDMIC) is presented. Largely, the EMDMIC consists of the three main modules: “Factors”, “Ecosystem Modelling” and “Management”. Functionality of each module is articulated in the paper. At the current stage of architectural design, the principles of multi-layered designs and platform independence have been applied. The latter enable to keep the options for future implementations of the tool open and also makes it potentially suitable for various targeting environments.