This paper presents a decision-making approach towards adaptive setup planning that considers both the availability and capability of machines on a shop floor. It loosely integrates scheduling functions at the setup planning stage, and utilizes a two-step decision-making strategy for generating machine-neutral and machine-specific setup plans at each stage. The objective of the research is to enable adaptive setup planning for dynamic job shop machining operations. Particularly, this paper covers basic concepts and algorithms for one-time generic setup planning, and run-time final setup merging for dynamic machine assignments. The decision-making algorithms validation is further demonstrated through a case study.