The end of Moore’s law and Dennard scaling emphasizes the need for application-specific computing architectures to achieve high resource and energy efficiency and real-time performance. The concept of a silicon compiler remains an enduring aspiration for design time reduction. In order to generate hardware implementations at register transfer level from behavioral descriptions, design automation tools must address challenging and interdependent problems, including allocation, scheduling, and binding. Additionally, manual intervention by the user is necessary to balance the resources vs. performance tradeoff via, for example, function inlining or loop unrolling/pipelining. Existing approaches typically solve these problems sequentially, compromising optimality in favor of simplicity and runtime. Here we show how to model the whole model-based design flow as one holistic integer linear programming (ILP) formulation aiming at consistently deriving the optimal microarchitecture for any given application. Incorporating clock gating minimizes the number of useless operations with negligible resource overhead (if any), while always guaranteeing optimal throughput. The unified nature of the proposed ILP model enables implementations unmatched by state-of-the-art approaches in terms of resource efficiency and measured power consumption. These results facilitate a streamlined design flow for highly optimized embedded systems in the context of model-based design.