CO2-rich gas injection into natural gas hydrate reservoirs is proposed as a carbon-neutral, novel technique to store CO2 while simultaneously producing CH4 gas from methane hydrate deposits without disturbing geological settings. This method is limited by the mass transport barrier created by hydrate film formation at the liquid–gas interface. The very low gas diffusivity through hydrate film formed at this interface causes low CO2 availability at the gas–hydrate interface, thus lowering the recovery and replacement efficiency during CH4-CO2 exchange. In a first-of-its-kind study, we have demonstrate the successful application of low dosage methanol to enhance gas storage and recovery and compare it with water and other surface-active kinetic promoters including SDS and L-methionine. Our study shows 40–80% CH4 recovery, 83–93% CO2 storage and 3–10% CH4-CO2 replacement efficiency in the presence of 5 wt% methanol, and further improvement in the swapping process due to a change in temperature from 1–4 °C is observed. We also discuss the influence of initial water saturation (30–66%), hydrate morphology (grain-coating and pore-filling) and hydrate surface area on the CH4-CO2 hydrate swapping. Very distinctive behavior in methane recovery caused by initial water saturation (above and below Swi = 0.35) and hydrate morphology is also discussed. Improved CO2 storage and methane recovery in the presence of methanol is attributed to its dual role as anti-agglomerate and thermodynamic driving force enhancer between CH4-CO2 hydrate phase boundaries when methanol is used at a low concentration (5 wt%). The findings of this study can be useful in exploring the usage of low dosage, bio-friendly, anti-agglomerate and hydrate inhibition compounds in improving CH4 recovery and storing CO2 in hydrate reservoirs without disturbing geological formation. To the best of the authors’ knowledge, this is the first experimental study to explore the novel application of an anti-agglomerate and hydrate inhibitor in low dosage to address the CO2 hydrate mass transfer barrier created at the gas–liquid interface to enhance CH4-CO2 hydrate exchange. Our study also highlights the importance of prior information about methane hydrate reservoirs, such as residual water saturation, degree of hydrate saturation and hydrate morphology, before applying the CH4-CO2 hydrate swapping technique.