The application of multi-floor manufacturing (MFM) in huge cities is related to the rational use of urban areas and the solution to traffic problems. The operation of the city MFM clusters depends on the efficiency of production and transport management considering technical, economic, environmental, and other factors. The primary goal of this paper was to identify and analyze the drivers of sustainable supply chains (SSCs) that influence or encourage the design of sustainable processes in city MFM clusters under uncertainty in supply chains. This paper presents an SSC performance model for city MFM clusters under uncertainty. The proposed model is universal and is based on material flow analysis (MFA) methodology. The presented analysis helps to determine the conditions for rhythmic deliveries with the use of the multi-IRTs. The coefficients of rhythmic deliveries for multiple intelligent reconfigurable trolleys (IRTs) and the capacity loss of freight elevators allow us to periodically assess the sustainability processes in city MFM clusters related to the flow materials. These assessments are the basis for the decision-making and planning of SSCs.