Serpentinization of peridotite provides a significant source of energy for the subseafloor biosphere and abiotic organic synthesis. The presence of diverse micrometer-scale organic matter in serpentinites offers insights into deep carbon cycling and the origin of life on Earth. It is critical to maintain stringent lab protocols in analyzing serpentinite samples, limiting the contact with organic materials that could contaminate serpentinites and cause misinterpretations. However, the extent to which these organic materials (e.g. latex gloves or nylon polishing disc) can introduce contamination remains unclear. Here we subject serpentinite samples from the Yap Trench in the western Pacific Ocean to multi-stage cutting and polishing procedures prior to analysis. Our findings from electron microscopy reveal that micrometer-scale organic matter in serpentinites is randomly distributed either on the sample surface or within Cr-spinel fractures. Further analysis using Raman spectroscopy indicates that the organic matter contains several hydrogen bonding moieties, similar to those found in the latex gloves or nylon polishing disc used during the treatment of serpentinite samples. Our results suggest that the detected organic matter is likely due to contamination from the organic materials involved during sample processing. Thus, future studies need to carefully assess micrometer-scale organic contamination and limit the use of organic materials when analyzing organic compounds hosted in serpentinites, not only on Earth but also on other rocky planets.