With wearable sensors, the acquisition of physiological signals has become affordable and feasible in everyday life. Specifically, Photoplethysmography (PPG), being a low-cost and highly portable technology, has attracted notable interest for measuring and diagnosing cardiac activity, one of the most important physiological and autonomic indicators. In addition to the technological development, several specific signal-processing algorithms have been designed to enable reliable detection of heartbeats and cope with the lower quality of the signals. In this study, we compare three heartbeat detection algorithms: Derivative-Based Detection (DBD), Recursive Combinatorial Optimization (RCO), and Multi-Scale Peak and Trough Detection (MSPTD). In particular, we considered signals from two datasets, namely, the PPG-DALIA dataset (N = 15) and the FANTASIA dataset (N = 20) which differ in terms of signal characteristics (sampling frequency and length) and type of acquisition devices (wearable and medical-grade). The comparison is performed both in terms of heartbeat detection performance and computational workload required to execute the algorithms. Finally, we explore the applicability of these algorithms on the cardiac component obtained from functional Near InfraRed Spectroscopy signals (fNIRS).The results indicate that, while the MSPTD algorithm achieves a higher F1 score in cases that involve body movements, such as cycling (MSPTD: Mean = 74.7, SD = 14.4; DBD: Mean = 54.4, SD = 21.0; DBD + RCO: Mean = 49.5, SD = 22.9) and walking up and down the stairs (MSPTD: Mean = 62.9, SD = 12.2; DBD: Mean = 50.5, SD = 11.9; DBD + RCO: Mean = 45.0, SD = 14.0), for all other activities the three algorithms perform similarly. In terms of computational complexity, the computation time of the MSPTD algorithm appears to grow exponentially with the signal sampling frequency, thus requiring longer computation times in the case of high-sampling frequency signals, where the usage of the DBD and RCO algorithms might be preferable. All three algorithms appear to be appropriate candidates for exploring the applicability of heartbeat detection on fNIRS data.