Amorphous orpiment-like As-sulfides (As2S3) are the most common As phases precipitating in hydrothermal systems, yet there is a lack of information regarding their solid-state characterization. Using a combination of optical, SEM–EDS, micro-Raman and XANES/EXAFS applications, we investigated yellow-orange As- and S-rich sediments occurring in the shallow-water hydrothermal system off the coast of Milos Island, Greece. The precipitates have several morphologies, but are dominantly colloidal. Intriguing “biological” morphologies also exist (e.g., cell-like (~ 10 μm), spirals (~ 20 μm), and rounded “cinnamon bun” shapes (~ 20 μm)). SEM–EDS data indicated that the precipitates have an As:S ratio similar to orpiment (average = 0.58, range 0.51–0.63; n = 8). Micro-Raman spectra indicated that orange colored precipitates appear to be dominated by poorly crystalline and/or amorphous arsenic sulfides with micro-amounts of more crystalline orpiment and impure sulfur. The yellow sediments also contained crystalline elemental sulfur in the form S8. Bulk As K-edge XANES spectra of the As-sulfide precipitates proved a valence of As corresponding to orpiment-type (As2S3) compounds (− 1 to + 3). EXAFS fitting results indicated that the studied material exhibits an amorphous orpiment-like structure with As ions coordinated by 3 sulfur atoms (CN = 3.0). The As–S interatomic distance of the first shell is calculated at 2.279 Å and the Debye–Waller factor (σ2) is 0.00427. These data suggest that the modeled structure of the studied precipitates is slightly S-deficient and ordered only in the first shell around As, resembling an orpiment-type structure, whereas higher shells are not present and must be disordered. The disorder phenomenon may be strictly produced either by the existence of occasional As–S–As bridges with As–As bonds or by the occurrence of As–O–As bridges, causing twisting of the AsS3 pyramids in the initial orpiment structure. This distortion in the higher coordination shells of the structural sheets creates the amorphous orpiment.