Here we present a method for compositional analysis of complex mixtures comprising nine compounds per sample at varying percentages. The compounds in each group possess comparable physical and chemical characteristics such as weight, hydrophilicity, and charge distribution, which are standard distinguishing factors in most analytical methods. Some compounds have the same chemical formula but differ in stereochemistry (four compounds) or constitutional isomers (three compounds), making separation challenging for typical analysis methods. We developed a high throughput autonomous MicroED approach to enable identification of all constituents and their relative ratios, mostly with high accuracy of just a few percent of their total composition. To demonstrate the extension of MicroED's capabilities using this approach, we further applied the method to an additional mixture. We identified all the ingredients in a mixture of nine compounds with a wide distribution of amounts per weight in the composition, with the smallest amount of constituents being around 3% by total mass.