Electronic banking is the modern trend in the banking industry. It has provides banking services to customers with satisfaction and enthusiasm. Irrespective of the delight in the electronic banking, many customers detest its introduction in the banking system due to the new frauds associated with it which is devastating. A lots of security measures have been put in place to combat the challenges, but this has not satisfactorily solve the problems. The introduction of biometric security offers a better alternative to combating security issues associated with electronic banking, but the application of biometrics in real time processing with heavy databases slows the processing speed. This does not suit banking operations. This paper discuses electronic banking, biometrics security, application of biometric security in real time processing, challenges with the application of biometrics security in real time systems, as well design an algorithm using Divide-And-Conquer algorithm technique with Merg Sort method that provides enhanced platform for smart application of biometrics security in electronic banking. The system so designed employs two databases, two servers, which are used in keeping bank customer’s biometrics records only in a database and the other records without the biometrics in another database. Bothe databases are run separately in different servers, while the sorted data are collated and presented as a customer’s page for authentication of customers as well as other banking services if authenticated.