Nitrogen metabolism is important for physiological processes during normal growth and development, as well as plant defence responses. Second‐stage juveniles of the cyst nematode Heterodera schachtii penetrate into the root and initiate permanent feeding sites called syncytia, from which they draw all necessary nutrients. To unravel whether the cyst nematode infestation changes nitrogen metabolism, the enzymatic activity and gene expression of nitrate (NIA) and nitrite (NIR) reductases and glutamate dehydrogenase (GDH), as well as levels of the metabolites nitrates, nitrites, and ammonium ions were estimated both locally in inoculated roots and systemically in shoots of inoculated Arabidopsis thaliana plants at 3, 7, and 15 days post‐inoculation (dpi). Moreover, gene expression of long hypocotyle 5 (HY5), a basic‐region leucine zipper (bZIP) transcription factor, was also determined, to learn more about the potential transcriptional regulation of the analysed enzymes. It was shown that the activity of nitrogen‐related enzymes and the content of metabolites fluctuated during the whole period of infection. These results were accompanied by organ‐specific and dpi‐dependent gene expression patterns. The high gene expression level of HY5 in infected roots at 7 and 15 dpi coexisted with enhanced expression of NIA1 and NIR1 at 7 dpi and NIA2 at 15 dpi. Enhanced HY5 expression level in shoots of infected plants at 15 dpi was followed by up‐regulation of NIA1 expression, suggesting that HY5 may regulate the gene expression of NIA and NIR during nematode infection. Our results indicate that changes in plant nitrogen metabolism occur during cyst nematode infection.