Elucidating compositions of the first cell membranes requires experiments with molecules and chemical conditions representative of early Earth. The molecules used are described as ‘prebiotically plausible’, i.e., they could have formed through abiotic reactions before the emergence of biology. Similarly, the chemical properties of solutions in which these membranes are formed (e.g., pH, temperature, ionic strength) must represent early Earth environments. Here, using confocal and transmission electron microscopy combined with population morphometry, we show that prebiotically plausible molecules, in solutions representative of Hadean submarine alkaline hydrothermal vents, form microstructures with substantial morphological diversity. The microstructures hold the potential for use as analogues of prebiotic processes in the rock record. Additionally, many of the structures are morphologically similar to purported early microfossils, highlighting limitations of morphological interpretation in these studies. Detailed analyses of abiotic microstructures are essential for understanding the earliest life on Earth, and for interpretation of potential biosignatures from extra-terrestrial bodies.