The use of willow plantations can be a sustainable approach for treating primary municipal wastewater, potentially reducing both the environmental and economic burdens associated with conventional treatment. However, the impact of wastewater irrigation upon the willow biorefinery potential has not yet been established. To investigate this effect, three-year-old field grown willows were harvested from plots kept as either controls or irrigated with primary municipal wastewater effluent at 29.5 million L ha^-1 yr^-1. Biomass compositional analysis, ionic liquid pretreatment and enzymatic saccharification were assessed and differential abundance of persistent extractable phytochemicals was evaluated using untargeted metabolite profiling. Glucan significantly increased by 8% in wastewater treated trees, arabinose and galactose were significantly decreased by 8 and 29%, respectively, while xylose, mannose and lignin content were unaltered. Ionic liquid pretreatment and enzymatic saccharification efficiencies did not vary significantly, releasing >95% of the cell wall glucose and recovering 35% of the lignin. From a total of 213 phytochemical features, 83 were significantly depleted and 14 were significantly enriched due to wastewater irrigation, including flavonoids and lignan derivatives. Considered alongside increased biomass yield from wastewater irrigation (+200%), lignocellulosic bioenergy yields increased to 8.87 t glucose ha^-1 yr^-1 and 1.89 t ha^-1 yr^-1 recovered lignin, while net extractives yields increased to 1.48 t ha^-1 yr^-1, including phytochemicals of interest. The maintenance of glucose accessibility after low-cost ionic liquid pretreatment is promising evidence that sustainable lignocellulose bioenergy production can complement wastewater treatment. Untargeted metabolite assessment revealed some of the phytochemical toolkit employed by wastewater irrigated willows, including accumulation of flooding and salinity tolerance associated flavonoids glabraoside A and glabrene. The extractable phytochemicals underpin a novel high biomass phenotype in willow and, alongside lignocellulosic yields, could help enhance the economic feasibility of this clean wastewater treatment biotechnology through integration with sustainable biorefinery.