A new series of bioconjugation ready naphthalene based azo fluorescent quenchers (naph-AFQs) has been developed as synthetically accessible alternatives to BHQ-2s. The target compounds were designed to retain the broad, red shifted absorption characteristics of BHQ-2 while improving compatibility with continuous flow synthesis. Initial batch studies confirmed the feasibility of the two step diazotisation azo coupling sequence but also revealed significant challenges associated with diazonium instability, solubility limitations, and product purification. To address these limitations, the synthesis was translated to a telescoped continuous flow process in which the hazardous diazonium intermediate is generated and consumed in situ, thereby improving operational safety, reproducibility, and process efficiency. An initial Design of Experiments (DoE) approach identified key parameters governing both diazotisation and azo coupling, enabling qNMR yields of 30-41% in the integrated flow process, comparable to the combined yield of the corresponding batch sequence despite elimination of intermediate isolation and purification. Process intensification through increased flow rates enabled throughputs of up to 5 g h-1 across multiple naph AFQ derivatives, while further concentration based intensification afforded naph-AFQ 14 at 14.7 g h-1 with 97% purity. All six naph-AFQs exhibited strong visible region absorption (λmax = 534-548 nm) and high molar extinction coefficients (2.4-3.1 × 104 M-1 cm-1), closely matching the photophysical characteristics of BHQ-2s and confirming their suitability as broad band quenchers for fluorescence based assays and diagnostics. Overall, this work demonstrates how continuous flow processing can overcome longstanding safety and efficiency challenges associated with diazonium chemistry while providing practical access to high value azo fluorescent quenchers for molecular biology, diagnostics, and bioconjugation applications.