Atmospheric trace gases such as dihydrogen (H<sub>2</sub>), carbon monoxide (CO) and methane (CH<sub>4</sub>) play important roles in microbial metabolism and biogeochemical cycles. Analysis of these gases at trace levels requires reliable storage of discrete samples of low volume. While commercial sampling vials such as Exetainers® have been tested for CH<sub>4</sub> and other greenhouse gases, no information on reliable storage is available for H<sub>2</sub> and CO. We show that vials sealed with butyl rubber stoppers are not suitable for storing H<sub>2</sub> and CO due to release of these gases from rubber material. Treating butyl septa with NaOH reduced trace gas release, but contamination was still substantial, with H<sub>2</sub> and CO concentrations in air samples increasing by a factor of 3 and 10 after 30 days of storage in conventional 12 mL Exetainers. Among the rubber materials tested, silicone showed the lowest potential for H<sub>2</sub> and CO release. We thus propose to modify Exetainers by closing them with a silicone plug, and sealing them with a stainless steel bolt and O-ring for long-term storage. Such modified Exetainers exhibited stable concentrations of H<sub>2</sub> and CH<sub>4</sub> exceeding 60 days of storage at atmospheric and elevated (10 ppm) concentrations. The increase of CO was still measurable, but nine times lower than in conventional Exetainers with treated septa, and can be corrected for due to its linearity by storing a standard gas alongside the samples. The proposed modification is inexpensive, scalable and robust, and thus enables reliable storage of large numbers of low-volume gas samples from remote field locations.