Nitrification is a major process within the nitrogen (N) cycle leading to global losses of N, including fertiliser N, from natural and agricultural systems and producing significant nitrous oxide emissions. One strategy for mitigation of these losses involves nitrification inhibition by plant-derived biological nitrification inhibitors (BNIs). Cultivation-based studies of BNIs, including screening for new compounds, has predominantly investigated inhibition of a single ammonia-oxidising bacterium (AOB), Nitrosomonas europaea, even though ammonia oxidation in soil is usually dominated by ammonia-oxidising archaea (AOA), especially in acidic soils, and AOB Nitrosospira sp., rather than Nitrosomonas, in fertilised soils. This study aimed to assess the sensitivity of ammonia oxidation by a range of AOA and AOB pure cultures to BNIs produced by plant roots (methyl 3-(4-hydroxyphenyl) propionate, sakuranetin and 1,9-decanediol) and shoots (linoleic acid, linolenic acid and methyl linoleate). AOA were generally more sensitive to BNIs than AOB and sensitivity was greater to BNIs produced by shoots than those produced by roots. Sensitivity also varied within AOA and AOB cultures and between different BNIs. In general, N. europaea was not a good indicator of BNI inhibition and findings therefore highlight the limitations of use of a single bioassay strain and suggest use of a broader range of strains that are more representative of natural soil communities.