The cloud-based logistics services allow cost reduction, higher elasticity, flexibility, and maximum utilization of resources for performing high computations and data analytics. Logistics and security are complex issues with the corporate entities when these are to be used for taking critical issues. To understand these, this paper discusses a conceptualized, flexible security framework for cloud-driven digital supply chain in Agricultural. Moreover, a security enhancement layer is included at each layer of the cloud with a feasibility study on protecting user information in the logistics services ambiance. Also, the Data Residency for cloud-based logistics services is elaborated with Data Security analysis. Further, the article discusses the possible solutions to handle the security concerns of the logistic model.