Variability represents an important challenge in multi-tenant SaaS applications. In fact, even if multi-tenancy realizes SaaS providers dream of having a single maintained software instance serving multiple customers (tenants) for common functionality, variations in tenants needs and their specific requirements at many places of the application bring providers back to the real world. They face an additional design concern: supporting application variability on a pertenant basis. In this paper, we focus on such variability concern and try to reduce its complexity by decoupling its management through different application layers. We rely on a two-steps decoupling approach: the first step consists of representing application variations as an explicit variability model while the second step consists of choosing the must appropriate application layer(s) to manage each variation. Our approach is illustrated by relying on a case study from the food industry.