The formation of nitrogen-containing compounds in bio-oil during microwave pyrolysis of Chlorella and Spirulina microalgae has been investigated in this study. Activated carbon (AC) and magnetite (Fe3O4) were used as microwave receptors during microwave pyrolysis experiments. It has been found that the use of Fe3O4 increased the total yield of bio-oil. The use of different microwave receptors did not seem to have affected the total yield of nitrogen-containing compounds in the bio-oil. However, Fe3O4 promoted the formation of nitrogen-containing aliphatics, thereby reducing the formation of nitrogen-containing aromatics. The use of AC promoted the dehydration reactions during amino acid decomposition, thereby enhancing the formation of nitrogen-containing aromatics during pyrolysis. From the gas chromatography-mass spectrometry (GC-MS) analysis results, the major high-value nitrogen-containing compounds in the pyrolysis bio-oil of Chlorella and Spirulina were identified as indole and dodecamide. The formation mechanisms of nitrogen-containing compounds were proposed and discussed.