This special issue of the Journal of Computer and System Sciences follows the 2013 International Conference on E-Business Engineering which was held at Coventry University, UK in September 2013. The conference attracted more than 100 researchers from all over the world and yielded many excellent presentations as well as thought-provoking discussions in the area of e-business engineering. Our interpretation of e-business engineering included the development of innovative systems of communication and operation between businesses and customers as well as state-of-the-art systems developed to create efficiency and support of business operation. Two pertinent topic areas were selected to be addressed in this special issue: (1) optimisation of systems; and (2) security, privacy and trust in systems. The authors of selected contributions from the conference have provided extended papers in order to create an interesting special issue which exposes many useful directions towards solving some of the current issues in e-business systems. E-business touches all of our lives. The exploitation of broadband and high connectivity has yielded a plethora of business services, from manufacturing, retail and finance, to education, health and social networking. Multimedia communication is growing and so too the need for ever-increasing bandwidth. Two important challenges facing e-business are: (1) optimisation to ensure that services can continue to grow without reducing quality; and (2) security ensuring that we can safely use internet systems without compromise to our valuable data assets and our privacy. This special issue contains papers which describe some of the issues faced and offer solutions to them.