Methods, non-transitory computer readable media, access policy management apparatuses, and enterprise network systems that facilitate adaptive organization of web application access points in webtops are disclosed. With this technology, access points for web applications are more effectively presented in webtops to facilitate more efficient access to web applications by clients. In particular, this technology utilizes historical application access pattern data to determine a subset of allowed web applications most likely to be accessed in a current session, and generates and provides a webtop with access points for web applications organized based on the determined subset of the allowed web applications. Thereby, this technology facilitates adaptive webtops that reduce the amount of time required to locate access points for web applications and improve user productivity.