Bright biocompatible fluorescent imaging dyes with red to near-infrared (NIR) emissions are ideal candidates for fluorescence microscopy applications. Pyrene–benzothiazolium hemicyanine dyes are a new class of lysosome-specific probes reported on recently. In this work, we conduct a detailed implementation study for a pyrene–benzothiazolium derivative, BTP, to explore its potential imaging applications in fluorescence microscopy. The optical properties of BTP are studied in intracellular environments through advanced fluorescence microscopy techniques, with BTP exhibiting a noticeable shift toward blue (λ_em ≈ 590 nm) emissions in cellular lysosomes. The averaged photon arrival time (AAT)-based studies exhibit two different emissive populations of photons, indicating the probe’s dynamic equilibrium between two distinctively different lysosomal microenvironments. Here, BTP is successfully utilized for time-lapse fluorescence microscopy imaging in real-time as a ‘wash-free’ imaging dye with no observed background interference. BTP exhibits an excellent ability to highlight microorganisms (i.e., bacteria) such as Bacillus megaterium through fluorescence microscopy. BTP is found to be a promising candidate for two-photon fluorescence microscopy imaging. The two-photon excitability of BTP in COS-7 cells is studied, with the probe exhibiting an excitation maximum at λ_TP ≈ 905 nm.