The potential to increase the life span of tools applied in cheese cutting machines is of great importance, considering their cost and the risk of fragmented metallic parts of the tool being inserted into the cheese. Such tools are commonly manufactured using stainless steel 405 and are subjected to dynamic loads during their operation, leading to fatigue failure. An efficient method to improve the fatigue properties of such tools is the application of micro-blasting. In this work, for the first time, an experimental–analytical methodology was developed for determining optimum micro-blasting conditions and ascertaining a preventive replacement of the tool before its extensive fracture. This methodology is based on the construction of a pneumatic system for the precise cutting of cheese and simultaneous force measurements. Additionally, the entire cheese-cutting process is simulated by appropriate FEA modeling. According to the attained results, micro-blasting on steel tools significantly improves the resistance against dynamic loads, whilst the number of impacts that a tool can withstand until fatigue fracture is more than three times larger. Via the developed methodology, a preventive replacement of the tool can be conducted, avoiding the risk of a sudden tool failure. The proposed methodology can be applied to different tool geometries and materials.