Fe-oxidising microorganisms in deep-sea hydrothermal vent environments are often used as analogues for primordial life on Earth. In fact, Earth’s oldest purported microfossils are preserved as hematite filaments in a jasper rock dated between 4,160 and 4,280 million years and thought to have originated in a seafloor hydrothermal environment. However, the kinds of post-depositional processes that can alter their morphologies are not well-known, which has implications for recognizing morphologies of bona fide microbial origin in the deep-time rock record. Here we show more than ten morphological types of filamentous Fe-oxyhydroxide microstructures occur in Fe-oxide specimens from deep-sea hydrothermal vents in the southwest Indian Ocean, including thick and thin filaments with the following morphologies: parallel-alignments, branching and pectinate-branching, curved and straight, hollow to tubular, twisted and coated with botryoidal silica. Botryoidal silica mineralisation is documented on several filament morphotypes and exhibits pattern with spheroidal twins, circular concentricity, and cavities, whereas their elemental composition is dominated by Si, Fe, C, with minor S and halogens. Such patterns and substances point to an origin from chemically oscillating reactions, which provide a novel abiotic model, based on C and Fe cycling, to explain occurrences of botryoidal minerals grown onto deep-sea filamentous Fe-oxyhydroxide microstructures. The documented filamentous morphologies and new model for silica botryoid formation help to understand abiotic carbon cycling in marine and lacustrine environments, ancient filaments preserved in the geological record, as well as a basis to seek similar structures in deep-space settings.