Rapidly changing permafrost landscapes are a potential key terrestrial source of greenhouse gases (GHGs) at a global scale, yet, remain poorly characterized regarding GHG origins and environmental controls on emissions. Subsurface ice wedges, commonly found across many permafrost landscapes, harbor GHG-rich gas bubbles. Analyzing these bubbles aids comprehension of subzero temperature GHG formation in permafrost. The Batagay megaslump, Earth's largest known thaw slump in northern Yakutia, provides an opportunity to study mixing ratios and isotopic compositions of both GHGs and non-GHG in ice wedge samples from two stratigraphic units: the Upper Ice Complex (UIC) and the Lower Ice Complex (LIC). The Ar/N2/O2 compositions and bubble shapes indicated that the studied ice wedges were likely formed through dry snow and/or hoarfrost compaction, and microbial activity remained active after ice wedge formation. The high CO2 and CH4 mixing ratios and carbon stable isotope values suggested that CO2 and CH4 primarily originated from microbial sources. N2O showed an “exclusive relation” with CH4—meaning that high N2O is observed only when CH4 is low, and vice versa—and N2O mixing ratios vary at different depths. These findings suggest that GHG formation in ice wedges is not solely controlled by physiochemical conditions, but involves a complex interplay between microbial activity and environmental conditions. Our study contributes to a better understanding of the dynamics involved in GHG formation within degrading permafrost landscapes.