A lot of discussion on how to efficiently develop software by using agile methods in enterprises and what kind of implications enterprises face on their path towards enterprise agility exists in nowadays. This paper describes how Fuzzy Cognitive Maps (FCM) can be used as Computational Intelligence (CI) tools for Decision Support (DS) in reducing the risks of the implications in this adaptation or transformation process. Particularly, FCM are used in understanding the effect of a set of critical Agile Adoption Factors (AAF) proposed in literature in the success of adopting agile. A set of preliminary experiments have been conducted to show that AAF can be evaluated with the use of FCM and their effect on adoption success is validated in three specific contexts. The scenarios investigated show that a critical implication is corporate bureaucracy. Also, results indicate that some enablers are the project teams’ personal traits, such as collaborative attitude and readiness to change, as well as, the customers’ level of commitment. The proposed FCM model provides an insight on the usefulness of the method for assessing agile transformation success.