A rice mill produces rice and a variety of by-products, including broken rice, rice bran, and rice husk. Rice husk, in particular, has been widely utilized as a source of fuel to generate heat and electricity. Efficient conversion of the by-products into value-added products via an integrated resource-efficient (IRE) rice mill complex provides a strategic option for rice mills to remain competitive. However, in the face of increasing global demand for rice, optimal resource allocation has become a major challenge for rice enterprises, which operate multiple rice mills with different technologies and capacities. This work proposes a Multi-Site Resource Efficient (MSIRE) System, which is a model-based generic framework for the efficient management of the aforementioned complex, interacting issues. The MSIRE system has been proposed to (i) plan resource allocation and utility net-work at each site, (ii) screen and select the most suitable technology, (iii) determine the logistic network, and (iv) plan capacity expansion with the objective of maximizing overall profit. The eight different scenarios analyzed with the MSIRE framework demonstrate the tool's powerful capability to guide planners toward a profitable rice mill business. Because of its generic element, the MS IRE can also be applied to other types of industry.