Soil aggregates may stabilize carbon at mineral surfaces and in the interior, but resolving such micro-scale carbon (C) turnover at the intact interior of soil aggregates <2mm is challenged by C contaminations during sample preparation such as from resin embedding. Here we introduce a novel C-free embedding method using silica gel for water glass formation, and applied it to soil aggregates from a C3/C4 vegetation change soil chronosequence (4, 10 and 19 years of Miscanthus cropping on former C3 soil) for subsequent C turnover analyses using laser ablation isotope ratio mass spectrometry (LA-IRMS). We hypothesized that C-free embedding allows for the first time the comparison of C turnover at soil aggregates both at the interior and at the outer surface. We found that using water glass embedding enabled ẟ13C analyses via LA-IRMS in all parts of the sample. There was an enormous micro-scale heterogeneity in ẟ13C signals within the aggregates, which increased with cropping duration (-5.5 to 41.5‰). Noteworthy, after 19 years Miscanthus materials were still found preferentially at soil aggregate surfaces and hardly in interior parts, documenting slow aggregate turnover but also success of the embedding technique for future micro-scale C dynamic analyses in environmental samples.