Pelagic Crenarchaeota produce glycerol dibiphytanyl glycerol tetraethers (GDGTs) as membrane lipids, and the GDGT composition changes according to growth temperature. This forms the basis of the TEX₈₆ paleotemperature proxy. This ratio correlates with sea surface temperature (SST) despite the fact that Crenarchaeota are distributed through the water column. Therefore there must be mechanisms that transport the surface signal to sediments such as repackaging in fecal pellets, marine snow, mass falls after phytoplankton blooms, or daily migration. To study GDGT transport, we analyzed stomachs and intestines of Atlantic and Mediterranean decapods as they are one of the major megafaunal groups, are easy to sample, and occur in both pelagic and benthic environments. GDGTs were found in most decapods' guts. GDGT abundances are significantly lower in intestines, but TEX₈₆-derived temperatures are not significantly different between stomachs and intestines (<1°C), suggesting that TEX₈₆ values are not altered during gut transit. Atlantic decapods show no difference in TEX₈₆ values between benthic detritivors and pelagic predators. However, Mediterranean decapods show a substantial difference between macroplankton feeders and bentho-pelagic predators. This is probably related to the freshness of the material consumed. TEX₈₆-derived temperatures in Atlantic decapods are close to the SST around the time of sampling, in agreement with stomach content analysis that shows fresh organic matter being ingested. For Mediterranean decapods, TEX₈₆ temperatures are significantly higher than SST around the time of sampling. This can be partly attributed to the large variability between decapod specimens and the low amounts of fresh material found in their stomachs.