The furthering of scientific knowledge depends in part upon the reproducibility of experimental results. When experimental conditions are not set with sufficient precision, the resulting background noise often leads to poorly reproduced and even faulty experiments. An example of the catastrophic consequences of this background noise can be found in the design of strategies for the development of solutions aimed at preventing garlic paste greening, where reported results are contradictory. To avoid such consequences, this paper presents a two-step strategy based on the concept of experimental design. In the first step, the critical factors inherent to the problem are identified, using a Plackett–Burman experimental design, from a list of seven apparent critical factors (ACF); subsequently, the critical factors thus identified are considered as the factors to be optimized (FO), and optimization is performed using a Box and Wilson experimental design to identify the stationary point of the system. Optimal conditions for preventing garlic greening are examined after analysis of the complex process of green-pigment development, which involves both chemical and enzymatic reactions and is strongly influenced by pH, with an overall pH optimum of 4.5. The critical step in the greening process is the synthesis of thiosulfinates (allicin) from cysteine sulfoxides (alliin). Cysteine inhibits the greening process at this critical stage; no greening precursors are formed in the presence of around 1% cysteine. However, the optimal conditions for greening prevention are very sensitive both to the type of garlic and to manufacturing conditions. This suggests that optimal solutions for garlic greening prevention should be sought on a case-by-case basis, using the strategy presented here.