In the paper, the problem of chatter vibration detection in the milling process of carbon fiber-reinforced plastic is investigated. Chatter analysis may be considered theoretically based on data from impact test of an end mill cutter. However, a stability region obtained in such way may not agree with the real one. Therefore, this paper presents a method that can predict chatter vibrations based on cutting force components measurements. At the beginning, a stability lobe diagram is created to establish the range of experimental test in the plane of tool rotational speed and depth of cut. Next, an experiment of composite milling is performed. The experimentally-measured time series of cutting forces are decomposed with the use of the improved Hilbert–Huang transform (HHT). To detect chatter, statistical methods and recurrence quantification analysis (RQA) are used. However, much better results are obtained when new chatter indexes are proposed. The indexes, derived directly from the HHT and RQA methods, can be used to build an effective chatter prediction system.