Soil carbon sequestration, a climate change mitigation option for agriculture, can either increase or decrease as a result of land management change (LMC) and land use change (LUC). To estimate all greenhouse gas (GHG) exchanges associated with various agricultural systems, life cycle assessments (LCAs) are frequently undertaken. To date LCA practitioners have not had a well-defined procedure to account for soil C in their assessments and as a consequence it is often not included. In this study, various methods used to estimate soil C changes due to (i) LMC and (ii) LUC are examined to assess soil C accounting methodologies in the life cycle inventory (LCI) of agricultural LCAs. A compromise between accuracy and completeness in LCA methods is necessary. A ranking of the preference of soil C accounting methods is suggested based on user expertise and data quality. For large scale assessment, the timing of soil CO2 emissions should be taken into account. If indirect LUC is relevant, a sensitivity analysis of assessment methods should be conducted because the methods highly affect assessment results. A common soil C accounting method that can be easily applied in agricultural LCA needs to be established and an agreement on indirect LUC methods will facilitate the assessment of LMC and LUC within agricultural LCAs.