Agriculture is one of the main factors with a direct impact on the natural environment (soil, water and air). An increased interest in the environmental impact of agricultural production results is due to—among other factors—significant human interference in the natural circulation of nutrients, posing a potential threat to the balance of ecosystems. Under current conditions, it is necessary to develop comprehensive diagnostic methods to control production processes in a way that would reduce costs and environmental burden throughout the product’s life cycle. Only a holistic approach that integrates environmental and economic analysis meets the criteria of analysis complexity, which is one of the main goals of methodical analysis of sustainable development. The article presents the results of the integrated environmental and economic assessment of selected crops. Maize and rapeseed production were assessed using the life cycle assessment (LCA) and life cycle costing (LCC) methodologies. The analysis was carried out on farms representing plant- and animal-based farming types. The conclusion presented in the study was based on the data from a study group consisting of 69 private commercial farms located in two regions of Poland. The calculated carbon footprint of both of winter rape and grain maize production was found to be higher in animal farming types. Pig farming type presented the highest overall costs of these crops, based on the approach of the LCC. Inclusion of carbon sequestration to the assessment of greenhouse warming potential allowed for the reduction of the net global warming potential (GWP) impact associated with the production of the analyzed crops. In both crops, mineral fertilization was the main factor influencing both the total carbon footprint and the LCC.