Lengthening and diversifying crop rotations is an efficient strategy to reduce the use of fertilizers and pesticides, thereby improving the sustainability of cropping systems. To test this assumption, six innovative cropping system prototypes were designed, each introducing one or more agroecological practices, as alternatives to the 2-year sunflower (Helianthus annuus L.)–durum wheat (Triticum turgidum L. subsp. durum) rotation widespread in southwestern France. Two 3-year rotations were implemented at INRAE, Toulouse, from 2011 to 2016. The six prototypes were composed of two low-input cropping systems (with/without cover crops) and four very low-input cropping systems (including cultivar or species mixtures, each with/without cover crops). As compared to the sunflower–wheat rotation, the prototypes aimed at reducing the use of N fertilizers by 25% (low-input) and 50% (very low-input) and pesticides by 50%. A set of agronomic, environmental, technical, and socio-economic indicators was calculated to assess the different components of sustainability. The introduction of agroecological principles resulted in a clear reduction of the use of synthetic inputs as compared to the sunflower–wheat rotation. The treatment frequency index was decreased by 56, 18 and 39% for the low-input cropping systems, very low-input cropping systems with cultivar mixtures, and very low-input cropping systems with species mixtures, respectively. However, the profitability decreased with the diversification of cropping systems as the semi-net margin decreased for the three previous cropping systems (745, 696, and 438 €·ha−1, respectively, vs. 963 €·ha−1 for the sunflower-wheat rotation). Despite the costs of inputs, the short rotation remained the most profitable. Agroecological practices succeeded in reducing the dependence of cropping systems on synthetic inputs, but their implementation needs to be improved to achieve better economic performance, using both scientific knowledge and know-how of innovative farmers.