With modern global navigation satellite system (GNSS) signals, the FFT-based parallel code search acquisition must handle the frequent sign transitions due to the data or the secondary code. There is a straightforward solution to this problem, which consists in doubling the length of the FFTs, leading to a significant increase of the complexity. The authors already proposed a method to reduce the complexity without impairing the probability of detection. In particular, this led to a 50% memory reduction for an FPGA implementation. In this paper, the authors propose another approach, namely, the splitting of a large FFT into three or five smaller FFTs, providing better performances and higher flexibility. For an FPGA implementation, compared to the previously proposed approach, at the expense of a slight increase of the logic and multiplier resources, the splitting into three and five allows, respectively, a reduction of 40% and 64% of the memory, and of 25% and 37.5% of the processing time. Moreover, with the splitting into three FFTs, the algorithm is applicable for sampling frequencies up to 24.576 MHz for L5 band signals, against 21.846 MHz with the previously proposed algorithm. The algorithm is applied here to the GPS L5 and Galileo E5a, E5b, and E1 signals.