Among the most promising technologies for sustained drug delivery systems are core-shell nanofibres prepared by electrospinning. However, the most common method for the production of those, coaxial electrospinning, suffers from extremely low flow rates limiting the practical applications of such fibres. Emulsion electrospinning, on the other hand, enables the use of the high-throughput needle-less electrospinning devices for the production of the core-shell nanofibres with active pharmaceutical ingredients embedded and protected in their core. The development of such drug delivery systems for the applications in bone regeneration is further challenged by the need for the inorganic additives meant to stimulate the regeneration of the bone. The main objective of this work is to develop a high-throughput electrospinning method for the production of hybrid (organic-inorganic) and bioactive scaffolds needed for bone regeneration. We demonstrate the importance of the formulation, e.g., presence of surfactants, on the stability of the emulsion, and thus on electrospinning. Our work is an important step forward towards the high-throughput production of complex multi-material scaffolds for sustained drug delivery.