This paper describes the nitration of 2,4-dinitrotoluene (DNT) and its conversion to 2,4,6-trinitrotoluene (TNT) at a gram scale with the use of a fully automated flow chemistry system. The conversion of DNT to TNT traditionally requires the use of highly hazardous reagents like fuming sulfuric acid (oleum), fuming nitric acid (90–100%), and elevated temperatures. Flow chemistry offers advantages compared to conventional syntheses including a high degree of safety and simpler multistep automation. The configuration and development of this automated process based on a commercially available flow chemistry system is described. A high conversion rate (>99%) was achieved. Unlike established synthetic methods, ordinary nitrating mixture (65% HNO3/98% H2SO4) and shorter reaction times (10–30 min) were applied. The viability of flow nitration as a means of safe and continuous synthesis of TNT was investigated. The method was optimized using an experimental design approach, and the resulting process is safer, faster, and more efficient than previously reported TNT synthesis procedures. We compared the flow chemistry and batch approaches, including a provisional cost calculation for laboratory-scale production (a thorough economic analysis is, however, beyond the scope of this article). The method is considered fit for purpose for the safe production of high-purity explosives standards at a gram scale, which are used to verify that the performance of explosive trace detection equipment complies with EU regulatory requirements.