Mostly, precision agriculture applications include the acquisition and elaboration of images, and it is fundamental to understand how farmers’ practices, such as soil management, affect those images and relate to the vegetation index. We investigated how long-term conservation agriculture practices, in comparison with conventional practices, can affect the yield components and the accuracy of five vegetation indexes. The experimental site is a part of a long-term experiment established in 1994 and is still ongoing that consists of a rainfed 2-year rotation with durum wheat and maize, where two unfertilized soil managements were repeated in the same plots every year. This study shows the superiority of no tillage over conventional tillage for both nutritional and productive aspects on durum wheat. The soil management affects the vegetation indexes’ accuracy, which is related to the nitrogen nutrition status. No-tillage management, which is characterized by a higher content of soil organic matter and nitrogen availability into the soil, allows obtaining a higher accuracy than the conventional tillage. So, the users of multispectral cameras for precision agriculture applications must take into account the soil management, organic matter, and nitrogen content.