The practice of managing logistic business processes in companies has many examples when negative scenarios are realized in the course of events that are unforeseen at the planning stage, and ultimately lead to significant damage. These circumstances define the necessity to develop methods to reduce the risks of the negative impact of uncertainty or inadequate information, which is typical for the planning stage, on the final results. The paper describes methodological approaches to accounting uncertainty in models and methods which are used to plan logistics business processes in a company in order to reduce these risks. At the same time, in order to ensure that the plans are sound, it is proposed to form arbitrary reserves of allocated resources that compensate for uncertainty. Taking into account various types of the information situation at the planning stage, methods are proposed for determining appropriate levels of such reserves of allocated resources. The suggested methodological approaches to accounting uncertainty form a basis for building specific models and methodologies to be used for planning logistics business processes of various companies, given their features. These models and techniques are an important element in the digital transformation of logistics business processes. Their use leads to lower costs in the implementation of these processes.