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.