Using multiphoton microscopy (MPM), we demonstrated that effective inducing of two-photon excited luminescence and second-harmonic generation signals in nano/microparticles of clinoptilolite type of zeolite (CZ) by femtosecond near-infrared laser excitation can be successfully utilized in multiphoton imaging of the drug adsorption processes. Adsorption of photodynamic active dyes (hypericin, chlorin e6, methylene blue, and fluorescein) and their release from CZ pores in the presence of biomolecules, such as collagen from bovine Achilles tendon, albumin, and hemoglobin, were investigated by absorption and fluorescence spectrometry. To quantify the experimental results on hypericin release, here we use a kinetic curves fitting approach and calculate hypericin release rates in different environments. This approach allows to compare various mathematical models and uses more parameters to better characterize drug release profiles. In addition, magnetic CZ particles were fabricated and proposed as a promising material for drug delivery and controlled release in biological systems. Optical spectrometry and MPM are effective approaches that may reveal potential of natural zeolites in controlled drug delivery and biomedical imaging.