The production of biofuels—specifically bioethanol and biodiesel—from agricultural residues and lignocellulosic biomass constitutes a core pillar in transitioning toward a circular economy and decarbonizing the transportation and power sectors. This approach provides a sustainable strategy that transforms the environmental hazards of agricultural waste accumulation and open burning into an opportunity for clean energy capture and reduced fossil fuel reliance, all while avoiding the "food vs. fuel" dilemma associated with first-generation biofuels. The primary technical challenges stem from the structural complexity of lignocellulosic agricultural residues. Extracting fermentable sugars from recalcitrant cellulose and hemicellulose matrices demands energy-intensive and costly chemical and thermal pretreatment processes. Furthermore, enzymatic hydrolysis efficiency is often impaired by the formation of chemical inhibitors during lignin breakdown. In biodiesel synthesis, high free fatty acid (FFA) and moisture levels in agricultural waste oils severely hinder the transesterification process, increasing catalyst consumption and undesirable soap formation. Environmentally, the overall carbon offset can be compromised if substantial energy and water inputs are consumed during treatment, distillation, and purification stages. To overcome these engineering and biochemical hurdles, researchers have engineered advanced technological solutions. Prominent among these is the deployment of green pretreatment methods using ionic liquids and deep eutectic solvents (DES), paired with genetically tailored microbial strains and robust enzymes capable of co-fermenting both hexose and pentose sugars with high inhibitor tolerance. For biodiesel production, implementing solid heterogeneous catalysts, ultrasound-assisted transesterification, and membrane reactors has significantly boosted conversion yields while reducing separation and purification costs. This framework is reinforced by rigorous Life Cycle Assessments (LCA) and process heat integration to minimize the total carbon and water footprints, optimizing both environmental performance and economic viability. Al-Mustaqbal University – The First Private University in Iraq