Carbon-based nanoparticles (NPs) are widely used in nanotechnology. Among them, nanodiamonds (NDs) are suitable for biotechnology and are especially interesting for skin delivery and topical treatments. However, noninvasive detection of NDs within the different skin layers or analyzing their penetration ability is complicated due to the turbid nature of the tissue. The iterative multiplane optical properties extraction (IMOPE) technique detects differences in the optical properties of the measured item by a phase-image analysis method. The phase image is reconstructed by the multiplane Gerchberg–Saxton algorithm. This technique, traditionally, detects differences in the reduced scattering coefficients. Here, however, due to the actual size of the NDs, the IMOPE technique’s detection relies on absorption analysis rather than relying on scattering events. In this paper, we use the IMOPE technique to detect the presence of the NDs within tissue-like phantoms. In addition, we perform ex vivo pigskin experiments to estimate the penetration of the NDs to the different skin layers and show that their presence reduces at deeper layers. The significance signal of the NDs within the epidermis, dermis, and fat layers gradually reduces, with t test significance values that are smaller than 10–4, 10–3, and 10–2, respectively. The IMOPE results are corroborated by TEM results and Franz-cell experiments. These results confirm that the IMOPE profiled the skin-permeation of the NDs noninvasively.