Abstract The nature of the magma plumbing system of Large Igneous Provinces is still poorly understood. Among these exceptional magmatic events from Earth’s past, the end-Triassic Central Atlantic Magmatic Province (CAMP) and the end-Cretaceous Deccan Traps (Deccan) coincided in time with two of the most catastrophic biotic crises during the Phanerozoic. In order to constrain the architecture of their magma plumbing system, glomerocrysts containing abundant bubble-bearing melt inclusions from basaltic lava flows of both CAMP and Deccan were investigated via in situ geochemical and microstructural analyses. The analysed glomerocrysts, dominated by augitic clinopyroxene crystals, represent fragments of a crystal mush entrained by basaltic magmas before eruption. The analysed melt inclusions, consisting of an intermediate to felsic composition glass and CO2-bearing bubbles, represent relics of interstitial melts and fluids within a porous crystal framework forming the crystal mush. The different volume proportions between bubbles and whole inclusions reveal that melt entrapment occurred after volatile exsolution. The minimum observed bubble/inclusion fraction indicates that the CO2 concentration in CAMP and Deccan melts was at least 0.3 wt.%, consistent with a maximum entrapment pressure of about 0.5 GPa at CO2–H2O fluid-saturated conditions. The MgO-rich composition of host clinopyroxene crystals and whole rocks is in contrast with the SiO2-rich composition of (trachy-) andesitic to rhyolitic glass of melt inclusions, pointing to disequilibrium conditions. Thermodynamic and geochemical modelling shows that fractional crystallization alone cannot explain the evolved composition of glass in melt inclusions starting from their whole rock composition. On one side, the oxygen isotope composition of clinopyroxene crystals in glomerocrysts ranges from + 3.9 (± 0.3) to + 5.8 (± 0.3) ‰ and their sample-averaged oxygen isotope composition spans from + 4.4 (N = 10) to + 5.6 (N = 10) ‰, implying that glomerocrysts crystallized from mafic melts with normal (i.e., mantle-like) to slightly low δ18O values. On the other side, the oxygen isotope composition of glass in melt inclusions ranges from + 5.5 (± 0.4) to + 22.1 (± 0.4) ‰, implying that melt inclusions entrapped intermediate to felsic melts with normal (i.e., mantle-like) to extremely high δ18O values, typical of (meta-) sedimentary rocks. Some melt inclusions are compatible with fractionation from the same mafic melts that crystallized their host mineral phase, but most melt inclusions are compatible with variable degrees of crustal assimilation and partial mixing, potentially followed by minor post-entrapment isotope re-equilibration. In the CAMP, where sedimentary basins are abundant, (meta-) pelites and occasionally granitoids were the most likely assimilants. On the contrary, in the Deccan, where sedimentary basins are rare, granitoids and metapelites were the most likely assimilants. Oxygen isotope compositions of glass in melt inclusions, spanning from mantle-like to crust-dominated signatures, suggest that the CO2 within their coexisting bubbles likely derived partly from the mantle and partly from assimilated crustal materials. The investigated glomerocrysts and their bubble-bearing melt inclusions are relics of a multiphase (i.e., solid + liquid + gas phases) crystal mush revealing a dynamic evolution for the magma plumbing system of both CAMP and Deccan, where crystals, silicate melts and exsolved fluids coexisted and interacted through most of the transcrustal section.