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This study assessed the technical and economic feasibility of three waste valorisation technologies, anaerobic co-digestion (AcoD), struvite precipitation, and hydrothermal carbonisation (HTC) to strengthen the Water-Energy-Food Nexus in Windhoek, Namibia. Windhoek is a semi-arid city facing water scarcity, energy import dependency, and reliance on imported food and synthetic fertilisers. The study sought to understand the co-located waste streams from Meatco, Namibia Breweries (NamBrew), and Namibia Beverages (NamBev) to characterise waste streams and quantify resource recovery potential. The assessment considered two scenarios: valorisation conducted in isolation by each industry (Scenario A), and integrated co-digestion in a intergrated facility (Scenario B). Using stoichiometric equations and parameters from published resources, mass balance, resource recovery, and discounted cash flow analyses were conducted over a 20-year project life at a discount rate of 8%. The results showed that the integrated scenario could recover significant energy, nutrients, and solid fuel from the combined waste streams. Of the three industries, the Namibia Breweries’ waste valorisation facility was highly commercially viable with a short payback period due to the avoided Industrial Effluent Treatment (IET) levy, while the meat processor (Meatco) was marginally commercially viable and Namibia Beverages economically non-viable due to its dilute effluent. The integrated scenario was commercially unviable due to the high cost of the conveyance piping system. The study found that the primary driver for waste valorisation is avoidance of compliance costs, such as the IET levy, rather than the direct sale of valorised products. The study showed that in areas where industrial discharge is priced to reflect its actual treatment cost, private investments in circular economy infrastructure is an opportunity, even for developing nations. This is the first study to integrate AcoD, struvite precipitation, and HTC in a single TEA calibrated to an African industrial cluster and the results provide a repeatable assessment framework that other resource-constrained cities in Sub-Saharan Africa battling water, energy, and food insecurity can use.