Single crystal metal-free halide perovskites have received great attention in recent years owing to their excellent piezoelectric and ferroelectric properties. However, the nanotoxicity and piezoelectricity within the nanoscale of such materials have yet been reported for the demonstration of practical applications. In this work, the observation of intrinsic piezoelectricity in metal-free perovskite (MDABCO-NH4I3) films using piezoresponse force microscopy (PFM) is reported. A cytotoxicity test is also performed on MDABCO-NH4I3 to evaluate its low-toxic nature. The as-synthesized MDABCO-NH4I3 is further integrated into a piezoelectric nanogenerator (PENG). The MDABCO-NH4I3-based PENG (MN-PENG) exhibits optimal output voltage and current of 15.9 V and 54.5 nA, respectively. In addition, the MN-PENG can serve as a self-powered strain sensor for human–machine interface applications or be adopted in in vitro electrical stimulation devices. This work demonstrates a path of perovskite-based PENG with high performance, low toxicity, and multifunctionality for future advanced wearable sensors and portable therapeutic systems.