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Agricultural production is the main area of human activity that affects both food security and well-being, as well as the environment, in which people live. The modern economy tries to combine economic and environmental goals, because uncontrolled intensive production growth can lead to irreversible changes in the environment. This paper addresses the issue of evaluating one of the methods in search of the golden mean of sustainable agricultural production, on the example of the potato-microbiome interaction leading to the development of an innovative strategy of potato breeding and production. The aim was to apprise the economic and environmental effects of innovative potato cultivation with the use of beneficial microorganisms in Poland based on the field data. The data for the analyses were obtained from experimental field work carried out in 2021–2022 under the PotatoMetaBiome project. The analysis of the collected data allowed us to conclude that from the economic point of view, the most profitable was the strategy that included the use of practices based on synthetic means of production (with mineral fertilizers and chemical protection). On the other hand, the use of innovative preparations with beneficial microorganisms slightly increased the profitability in relation to the strategy without means of production and with the use of synthetic means of production. At the same time, it had the least negative impact on the environment than other agricultural practices. The obtained results indicate that the use of beneficial microorganisms may be a viable alternative agricultural strategy in potato production. It allows farmers to obtain satisfactory economic results while maintaining the environmental regime. Their use, however, requires further research in terms of the impact on the economics and organisation of agricultural production.