Energy systems have to deal with energy cost and environmental concerns such as greenhouse gas emission. Industrial buildings considered as Microgrid (µG) with heavy load worsen these issues even more. Further, cyber-attacks on the data communication channel between utility and customer is also a potential threat and may alter the data as well as the confidentiality of it, resulting in an inaccurate result. To address these problems, this paper proposes two-cored Building Energy Management System (BEMS) for Industrial Microgrid (IµG) with first cored termed as the energy layer concentrating on energy cost and emission reduction, while second cored termed as security layer provides the un-authorized intrusion detection and prevention system (IDS/IPS) for cyber secure communication of data. The µG under consideration contains national grid, Natural Gas (NG), solar Photovoltaic (PV) as input carriers; electrical energy at output ports; electric vehicle (EV) fleet; battery bank; solar PV panel as non-dispatchable Distributed Energy Resources (DERs) and Internal Combustion Engine (ICE), Fuel Cell (FC) and Micro Turbine (MT) as dispatchable DERs. Energy layer optimization problem has been solved in MATLAB using flower pollination algorithm for µG energy consumption cost and emission reduction. To develop and analyze the security layer, Linux operating system based Smooth-sec software has been used. Devised security layer continuously monitors the network traffic between customers and BEMS as well as BEMS and utility server. During monitoring it distinguish the licensed user or malicious attacker to detect and prevent possible internal and/or external intrusions in the communication channel. Results show that EMS reduces energy cost and emission in addition to cyber security from internal threats. Proposed two-cored control may be manufactured for utilities to realize its benefits for industrial customers in a smart energy distribution system.