Asphalt pavements are a critical component of modern infrastructure, and reducing their carbon footprint is a key goal in the industry. Bio-derived materials are being introduced into various bituminous binders, including polymer modified binders (PMBs), to improve sustainability. However, PMBs inherently face storage stability issues due to the addition of polymers like styrene-butadiene-styrene (SBS), typically addressed by using sulphur as a crosslinking agent. The addition of bio-oils can further impact storage stability, even with the use of crosslinking agents. This study investigates the use of bio-oil derived from industrial byproducts as an environmentally friendly extender in PMBs, focusing on how different incorporation methods affect the stability of the polymeric network and binder performance. Storage stability test was conducted to evaluate the effects of mixing methods on phase separation during hot storage with segregation values reduced from 35% to 6%. Preliminary results demonstrate that the bio-oil incorporation method significantly influences polymer network formation and its cross-linking, directly affecting storage stability. Some methods resulted in totally stable mixtures that maintained homogeneity, while others led to phase separation despite identical materials being used. This highlights the importance of optimising not only the materials and their dosage but also the mixing methodology to achieve bio-oil modified PMBs with improved storage stability. These findings support the increased use of bio-derived materials in the construction industry. They contribute to the development of more sustainable materials for transportation infrastructure, addressing both the demand for eco-friendly solutions and the challenges of material storage and handling.