Biologically-resistant carbon (C) comprises the bulk of C in most soils and is often estimated from chemical separation of a soil organic matter (SOM) fraction that is not hydrolysed by strong acid, and exhibits an older radiocarbon age and slower turnover than the whole SOM. Here we examine the effects of acid hydrolysis – the method used to separate the nonhydrolysable C – on the quantity, structure and isotopic makeup of C in pure model carbohydrates and those contained in senescent maize that resemble C inputs to SOM. We demonstrate that significant alterations occur during hydrolysis resulting in C mass losses (up to 75% preferential loss of 13C) and de novo synthesis of nonhydrolysable, 13C-depleted material dominated by aromatic > alkyl > carbonyl moieties. We infer that similar losses, and transformations of 14C, would partly explain the greater ages attributed to the chemically resistant C, seriously impairing the use of acid hydrolysis to identify this pool of SOM and that de novo synthesis during hydrolysis has obfuscated the true chemical nature of the nonhydrolysable fraction of SOM.