Agricultural land accounts for approximately 40% of the total Natura 2000 (N2K) network area. Therefore, many habitats and species protected under the Habitats and Birds Directives are dependent on or linked to agricultural practices. This implies that sustaining agriculture of a high natural value is a priority in achieving the aim of halting the loss of biodiversity in the European Union (EU). However, extensive agriculture is unprofitable in many regions of the EU, which results in it being either abandoned or intensified in the absence of financial support. Hence, organic farming (OF), which is most often supported with public funds, can be an alternative to conventional agriculture in N2K areas. This article is an empirical study of the differences in perceiving the possibilities of farm functioning in a protected area (PA) by organic and conventional farm owners. It was examined whether this could be the actual path to improving farmers’ living conditions in the context of legal protection of naturally valuable areas. The study material comprises the results of a survey conducted at the turn of 2016 and 2017, which addressed a total of 292 farmers, including 152 organic farm operators and 140 conventional farm operators, whose areas under cultivation were located within the N2K “Dolina Biebrzy” (“Biebrza Valley”) PLH200008 area in Poland. For the analysis of the data collected using structured questionnaires, a variety of statistical methods and techniques were applied. The study results indicated that in terms of satisfaction with the economic performance of their farms, there is no major difference between the opinions expressed by organic and conventional farm owners. However, organic farming could be an alternative livelihood strategy from the environmental policy perspective.