Azo fluorescent quenchers (AFQs) such as BHQ-2 and DABCYL are crucial components in bioanalytical and diagnostic applications due to their effective fluorescence quenching capabilities. Despite their widespread utility, their traditional batch synthesis is often limited by low yields, poor scalability, long reaction times, and safety concerns arising from unstable intermediates. This thesis explores continuous flow chemistry as a strategy to address these challenges, aiming to develop safer, more efficient, and scalable methods for AFQ synthesis. Chapter 2 investigates the synthesis of BHQ-2 derivatives. This chapter examines the challenges associated with both batch and continuous flow approaches, focusing on the influence of different substituents on synthetic yields and photophysical properties. It highlights key limitations such as the formation of undesired by-products and difficulties with diazonium salt stability, which restrict the feasibility of continuous flow telescoping for these compounds. The chapter concludes that while BHQ-2 remains a valuable target, alternative molecular scaffolds are needed to overcome these synthetic bottlenecks. Chapter 3 addresses this need by presenting the design and synthesis of novel naphthalene-based AFQs. The chapter details the development of a multistep telescoped continuous flow process capable of generating and immediately consuming unstable diazonium intermediates in situ. Through systematic optimisation, this chapter demonstrates improved safety, scalability, and throughput in the production of these new AFQs. The work showcases the potential of continuous flow methods to produce complex fluorescent quenchers with desirable photophysical properties more efficiently than batch synthesis. Chapter 4 focuses on the scalable synthesis of DABCYL-based AFQs using both single-step and multistep continuous flow techniques. It explores process optimisation and intensification strategies to achieve high yields and throughput, highlighting the economic and practical advantages of these flow systems. Additionally, this chapter discusses the future direction for incorporating greener solvents and more sustainable process designs to enhance the overall green chemistry profile. Together, the chapters of this thesis provide a comprehensive exploration of the challenges and opportunities in AFQ synthesis. They demonstrate how continuous flow chemistry can be harnessed to develop safer, faster, and more scalable synthetic routes for a variety of AFQs, laying the groundwork for future advances in fluorescent probe production with applications across diagnostics, biological research, and materials science.