The aim of the study was to provide the examples of eco-innovations in agriculture relating to the concept of sustainable development and the indication of their conditions. Quantitative and qualitative methods were applied to the research, namely: descriptive statistical and economic analysis of the Polish Farm Accountancy Data Network (FADN) data and Statistics Poland data, as well as case studies of organic food producers, covering the years 2005–2019. Indicated information sources, encompassing long time span of analysis and various data collections, allowed presenting the complementary picture of eco-innovations at the sector and farm levels. The research examined the different types of ecological innovations in Polish agriculture, including: (1) organisational innovations with an institutional background (e.g., the organic farming support and greening mechanism of the Common Agricultural Policy (CAP)—implemented in the family farming sector); and (2) the product, marketing, process and organisational innovations in selected organic farms that were individual farmers’ initiatives. On the one hand, the research documented the effectiveness of new agricultural policy solutions in the agricultural sector that are examples of organisational eco-innovations. During 2005–2016, the certification system, as well as policy support, contributed to the development of organic farms in Poland in terms of the growth in the share of this type of holdings in total (from 0.5% to 4.6%) and in the overall utilised agricultural area (UAA) (from 0.3% to 3.7%). Moreover, during 2014–2015, as a result of the greening in agricultural holdings, the area sown with pulses and papilionaceous, i.e., crops improving soil structure and protecting soils, rose by 174% and 161%, respectively. On the other hand, the case studies conducted showed that the food producers’ knowledge and skills combined with a favourable local economic and social situation, as well as institutional support, played a key role in the process of the emergence of eco-innovations. Among those factors, the respondents’ individual characteristics associated with attitudes towards farming and the social, human and physical capital passed on by family members should be highlighted. This paper contributes to existing literature in two ways. First, this study combines both quantitative and qualitative (including in-depth interviews) approaches to eco-innovations at the micro and macro level of analysis. Second, by differentiating two approaches to ecological innovations, namely the conventional and the sustainable, the article indicates and considers the key factors favourable to the latter.