The green pea (Pisum sativum L.) is an economically, nutritionally, and culturally important legume. It is a crop that is subject to various investigations due to its popularity with the development of various protocols in different topics, except for nano-biotechnological studies. This work was carried out to evaluate the uptake, distribution, translocation, and bioaccumulation of the single-walled carbon nanotubes (CNTs) and gold nanoparticles (AuNPs) within the economically important plant Pisum sativum morphologically and anatomically with a dark-field microscopy system. Data were analyzed for morphological parameters such as stem, tendril, root length, number, shape, width-length of the stipules, and root-stem-stipule. Our results proved the stimulation for growth and anatomical parameters such as CNTs aggregates and AuNPs particles at paranchyma, cortex, spongia cells, starch formation and accumulation in lenticels, stoma cells, and stomatal pores. In this study, we compared the utilization of the entire available Attenuated Total Reflectance—Fourier Transform Infrared Spectroscopy (ATR-FTIR) spectral range (525–4000 cm−1) for conducting principal component analysis (PCA) without excluding any specific spectral wavenumbers with the spectral range chosen based on larger PCA loadings. The results demonstrate that for both chosen spectral ranges of the PCA score plots, utilizing only the first three principal components (PCs), we effectively visually separated three groups: (1) plants treated with Au NPs, (2) plants treated with CNTs, and (3) control plants without nanoparticle treatment using ATR-FTIR spectral data from combined samples of root, stem, and leaves from the Pisum sativum plant. Our investigation shows that green pea, a species of the Fabaceae family, is low-cost, fast, and non-toxic and requires an environmentally safe process in the area of nanotechnology in bio-application regarding the green synthesis of nanoparticles; it is a step for green mining, phytoremediation, delivering drugs, and biomolecules. Our findings show that green pea and the Fabaceae family have more advantages for the biological synthesis of C-Au nanoparticles and guide soil health, agricultural development, pharmaceuticals, drug delivery science, and other types of medicinal investigations with a new approach, while a lot of economic plants in the Fabaceae family will be available for the green synthesis of more NPs with single and rapid protocols and will be a popular family in nano-biotechnological studies in the next few decades.