Continuous-flow inlets from oxidation reactors are commonly used systems for biological sample introduction into isotope ratio mass spectrometers (IRMS) to measure 13C enrichment above natural abundance. Because the samples must be volatile enough to pass through a gas chromatograph, silylated derivatization reactions are commonly used to modify biological molecules to add the necessary volatility. Addition of a tert-butyldimethylsilyl (TBDMS) group is a common derivatization approach. However, we have found that samples do not produce the expected increment in measured 13C abundance as the TBDMS derivatives. We have made measurements of 13C enrichment of leucine and glutamate standards of known 13C enrichment using derivatives without silicon (N-acetyl n-propyl ester), with silicon (TBDMS), and an intermediate case. The measurements of 13C in amino acids derivatized without silicon were as expected. The 13C enrichment measurements using the TBDMS derivative were higher than expected but could be corrected to produce the expected 13C enrichment measurement by IRMS if one carbon was removed per silicon. We postulate that the silicon in the derivative forms silicon carbide compounds in the heated cupric oxide reactor, rather than forming silicon dioxide. Doing so reduces the amount of CO2 formed from the carbon in the sample. Silylated derivatives retain carbon with the silicon and must be used carefully and with correction factors to measure 13C enrichments by continuous-flow IRMS.