Integration of energy efficiency measures, energy conversion, and renewable technologies is a proven pathway for reducing Scope 1 emissions. However, as integration increases, Scope 2 emissions from operations, Scope 3 emissions along the value chain, and overall costs also rise. Since most industries already report GHG emissions in line with the GHG Protocol (Scopes 1–3), the relative importance of Scope 2 and 3 is increasing. This makes lifecycle-aware integration strategies essential and highlights the need for companies to balance total annual emissions with total annual costs. Building on HSLU’s role as the competence center for Pinch Analysis in Central Switzerland, this project developed a robust and flexible framework that unites Pinch Analysis (PA), Life Cycle Assessment (LCA), and Multi-objective Optimization (MOO) into a single decision-support tool. The framework identifies technically feasible integration options, quantifies environmental impacts, and derives Pareto fronts that reveal trade-offs between emissions and costs under various resource constraints such as solar irradiance, access to clean electricity, biomass availability, etc. These results can be translated into actionable guidance for industry under real-world resource constraints. The framework was tested in two Swiss dairy case studies (continuous and non-continuous processes). Direct and indirect heat recovery formed the most cost-effective foundation. Heat pumps at low to medium temperatures achieved about 30% Scope 1 emission reduction with a 2.1-year payback. Solar thermal proved highly sensitive to solar irradiance, while biomass offered the deepest cuts, up to 82% reduction in baseline emissions, albeit with higher costs and payback times of up to 21 years. Combining technologies consistently outperformed single-technology solutions in terms of cost-effectiveness. The comparison of direct and indirect emissions across scenarios reveals a threshold integration beyond which the indirect Scope 2–3 emissions became dominant, underscoring the need for lifecycle-aware planning. The threshold was identified at 72% degree of integration for the case study in this work. Overall, the project emphasizes that decarbonization strategies must be evaluated not only on direct CO2 reductions but also on upstream and operational impacts. By combining PA, LCA, and MOO into a flexible framework, Eco-Targeting equips industries and policymakers with a structured approach to identify optimal integration strategies. Going forward, the framework can be extended to additional sectors and technologies, offering a robust tool to design cost-effective pathways toward net-zero.