The production of strawberry concentrate produces a side stream after extrusion that is commonly landfilled. This strawberry extrudate (SE), of lignocellulosic character, contains valuable bioactive compounds such as sugars and phenols. Thermal treatments, such as steam explosion, are currently used for the valorisation of agricultural lignocellulosic wastes due to their ability to impact the structure of the lignocellulose and hemicellulose present in these wastes, favouring the disruption of fibrous material. Steam explosion has already been shown as a promising technology for phenol recovery from SE. Biogas is an additional valuable resource that might be produced from thermally pretreated and de-phenolised SE. This study assessed the influence of a steam-explosion pretreatment and the subsequent recovery of phenolic compounds from the long-term operation of a semi-continuous anaerobic digester of pretreated SE. The anaerobic digestion of SE steam exploded at 220 °C for 5 min and de-phenolised was stable at an OLR of 0.5 g of volatile solids (VS)/(L·d), which permitted a specific production rate of 135 ± 11 mL of CH4/(g of VS d). The system was not able to operate at an OLR of 1 g of VS/(L·d), which resulted in a failure of the process. Despite the inhibition threshold of phenolic compounds not being achieved, the inhibition of the anaerobic digestion process at an OLR of 1 g of VS/(L·d) was most likely due to the overloading of the system. This was indicated by the accumulation of soluble organic matter and volatile fatty acids. The increase in the propionic acid concentration up to 1300 mg/L when operating at OLRs higher than 0.5 g of VS/(L·d) could be the main factor responsible for the inhibition. An economic evaluation showed that the proposed approach (steam explosion, phenol recovery, and anaerobic digestion) would offer positive benefits, taking into account the high phenolic recovery (0.90 g of gallic acid equivalents/kg of extrudate) and the low sales price of the phenol extract, i.e., EUR 0.610/g of gallic acid equivalents, needed to reach zero net profit.