In some studies, the researchers pretreated and measured organic carbon, nitrogen and their isotopes (δ13C and δ15N) of marine sediment together, to save costs and resources of analysis. However, the procedure of acidification to remove inorganic carbon for analysing δ13C can affect the values of nitrogen and δ15N, and the biases vary a lot depending on the CaCO3 contents of sediments. In this study, the biases of total nitrogen (TN) and δ15N values arising from acidified sediments were compared between the CaCO3-poor (1%–16%) and CaCO3- rich (20%–40%) samples. TN and δ15N values were altered during acid treatment (without centrifugation) that possibly led to N-containing compounds volatilization. For CaCO3-poor samples, acidification led to a range of 0%–40% TN losses and 0‰–2‰ shift in δ15N values; and 10%–60% TN losses and 1‰–14‰ shift in δ15N values for CaCO3-rich samples. The biases from most samples exceeded the precision of the instrument (0.002% for TN and 0.08‰ for δ15N), and high biases could mislead our judgment for the environmental implication of the data. Thus, avoiding co-analysis of organic carbon, nitrogen and their isotopes (δ13C and δ15N) in sediments, even for CaCO3- poor marine sediments, is necessary.