Fluorescence sensing through skin using wearable and cost-effective sensors can enable numerous biomedical applications, including continuous monitoring and quantification of biomarkers in conjunction with embedded fluorescent biosensors. Strong autofluorescence of the skin and its varying temporal response to excitation make it challenging to achieve highly sensitive fluorescence sensing at the visible part of the electromagnetic spectrum. Here, we demonstrate a compact, cost-effective and light-weight fluorescence imaging system for quantitative sensing through a highly autofluorescent, scattering and absorbing medium. We built a mobile fluorescence microscope weighing < 40 grams to sensitively quantify the concentration of fluorescent dyes through a skin tissue phantom. The optical characteristics of the skin phantom, such as scattering, absorption, and autofluorescence were designed to closely resemble the characteristics of human skin. In order to separate the target fluorescence emission signal from the tissue phantom’s autofluorescence we utilized an oblique Gaussian excitation profile, and performed our processing in the spatial frequency domain. Using an excitation intensity that is 8-fold below the safe exposure limit determined for human skin, we detected and quantified the concentration of Alexa 647 dye molecules in a microfluidic reservoir (with a volume of 0.01 µl) that is positioned 0.5 mm and 2 mm underneath our skin phantom, and achieved a detection limit of ~106 pg/ml and 5.3 ng/ml, respectively. Our method is also robust to lateral misalignments between the sample and the imaging device, with e.g., ~2-fold loss in limit of detection for ~0.6 mm lateral misalignment.