The aim of this study was to develop and validate a microtiter macro lens-coupled smartphone (MCS) assay for the quantitation of the total saponins in quinoa based on foam measurement. The 96-well micro plate with a black bottom and an inclination angle = 12.102° of macro lens-coupled smartphone allows to acquire images with a high resolution. The foam stability, a critical aspect for the MCS assay, was significantly improved by the inclusion of a chelating agent (EDTA 50 mmol L−1) and bovine serum albumin (0.5 mg mL−1). The MCS assay was linear within the range of 9.039–180.773 × 10−4 mg mL−1 of saponin (R2 = 0.9929), using the integrated density/area as a foam measurement (Y) and the logarithm of saponin concentration (X) (Y = 372.1 + 104.2LogX). The MCS assay was 50-folds more sensitive than afrosimetric assay -AA- with LOD = 3.168 × 10−4 mg mL−1 and LOQ = 4.784 × 10−4 mg mL−1. MCS assay was more reproducible (relative standard deviation (RSD) = 0.632–9.646%) than AA (RSD = 3.44–44.04%). The correlation analysis, Bland-Altman analysis and Passing-Bablok regression showed good agreement between total saponin content in quinoa as measured by the MCS assay and AA. Based on the green analytical procedure index, MCS assay can be considered as a green procedure.