The main objective of the present work is to evaluate the ISO 9001 Quality Systems in the smaller companies within the agriculture sector in Spain. In order to arrive at the main purposes of the present work, two evaluations were conducted. The first one before the current global financial crisis, and the second one will be done in the midst of the crisis. In addition, we provide the sector companies an original tool that facilitates the economic evaluation of their commitment by the Quality Systems. By comparing the value of the business under the assumption of whether or not it has implemented the ISO 9001 quality system, an approximation of the value that ISO 9001 certification has been obtained. Given the high uncertainty and subjectivity that the business valuation presents, discounted cash flow analysis in a fuzzy environment was used. The final results show that, despite being small businesses, in most of the analyzed cases the ISO 9001 quality system increases its contribution to the final value of the company. This is the case both before the current economic crisis and in the context of the crisis.