Engineering of land use systems for policy-oriented future studies and the development of new farming systems requires various information sources. Often, both process knowledge and data are subject to uncertainty that affects quantification of land use systems in their inputs and outputs. This paper analyzes the effects of uncertainty in three important N-relationships relevant for quantification of future-oriented cropping systems: (i) N-leaching as function of crop characteristics, (ii) N-concentration as function of yield level, and (iii) the recovery of crop residue-N. Based on verifiable assumptions, uncertainty in these three N-relationships is specified in terms of N-loss and production costs of cropping systems. Data and process knowledge as applied in LUCTOR, a summary model to design and quantify inputs and outputs of cropping systems for the northern Atlantic zone of Costa Rica, are used as a case study. All three relationships and their uncertainty have a major impact on N-loss of cropping systems, while effects on costs are limited and depend on the share of costs for fertilizer management in total production costs. Analyses as presented explicitly specify uncertainty of process knowledge and data used in future-oriented studies. Therefore, such analyses enable a better management or reduction of uncertainty through the identification of cropping systems with smaller uncertainty margins, and identification of research aimed at a more complete understanding of involved processes.