Soil acidity (pH <5.5) limits agricultural production due to aluminum (Al) toxicity. The primary target of Al toxicity is the plant root. However, symptoms can be observed on the shoots. This study aims to determine the potential use of chlorophyll fluorescence imaging, multispectral imaging, and 3D multispectral scanning technology to quantify the effects of Al toxicity on corn. Corn seedlings were grown for 13 days in nutrient solutions (pH4.0) with four Al treatments: 50, 100, 200, and 400 μM and a control (0μM AlCl3 L-1). During the experiment, four measurements were performed: four (MT1), six (MT2), 11 (MT3), and 13 (MT4)days after the application of Al treatments. The most sensitive traits affected by Al toxicity were the reduction of plant growth and increased reflectance in the visible wavelength (affected at MT1). The reflectance of red wavelengths increased more significantly compared to near-infrared and green wavelengths, leading to a decrease in the normalized difference vegetation index and the Green Leaf Index. The most sensitive chlorophyll fluorescence traits, effective quantum yield of PSII, and photochemical quenching coefficient were affected after prolonged Al exposure (MT3). This study demonstrates the usability of selected phenotypic traits in remote sensing studies to map Al-toxic soils and in high-throughput phenotyping studies to screen Al-tolerant genotypes.