In Europe, the lack of specific rules regulating organic vegetable production in protected conditions has led to the implementation of extremely diversified systems of production, at different level of intensification. In this study, we compared three strawberry organic production systems based on the following main criteria of soil fertility management: input substitution (SB), a simplified system of organic production that mimics conventional agricultural practices and two systems characterized by a more complex soil fertility management, based on the introduction, in the rotation of agroecological service crops (ASCs) and compost (AC), and of ASCs and cattle manure (AM). Strawberry yields, in the compared systems, were not significantly different in both years of our research, while, as a whole, the yield in 2013 (30.3 Mg ha−1) was significantly higher than in 2014 (28.9 Mg ha−1). Crop nitrogen (N) needs, during the entire cycle of production, were satisfied according to the same pattern by SB, AC and AM, while green manuring and organic amendments in AM and AC determined a higher soil organic N content, compared with SB. As far as the production quality is concerned, both AM and AC treatments yielded strawberry fruits similar to SB, but with better characteristics in terms of color and phenolic content. AM and AC did not differentiate statistically in the two year period of our research.