Nitrogen (N) fertilization affects wheat yield and grain protein concentration; however, its mismanagement can increase plant lodging. While the use of plant growth regulators such as trinexapac-ethyl (TE) can mitigate plant lodging, their effects on seed physiological quality are not well known. The aim of this study was to evaluate the effects of N fertilization and TE on wheat yield, lodging and seed quality of spring wheat varieties. It was carried out in the 2018 growing season in the environments of Londrina and Ponta Grossa, Brazil. A randomized complete block design was used with a 2 × 3 × 3 factorial arrangement to evaluate two wheat genotypes (WT 15008 and WT 15025), three top-dressing N rates (0, 40 and 120 kg ha−1), and three TE rates (0, 50 and 100 g ha−1). Agronomic characteristics related to wheat productivity (hectolitre weight, thousand-grain weight, density of fertile spikes, plant height, lodging and grain yield) and seed physiological quality (seed germination and vigour; length and dry matter of normal seedlings) were evaluated. Increasing N rates up to 120 kg ha−1 increased plant lodging up to 26.4 percentage points for WT 15025 in Londrina. TE impaired some traits of seed physiological quality. Spraying 100 g ha−1 TE on the plants reduced seedling length by 9.4% in the seeds of WT 15008 harvested in Ponta Grossa compared to the TE control (0 g ha−1). The dry matter of the seedlings from the seeds harvested in Londrina declined by 7.2% due to the application of 100 g ha−1 TE, compared to the control. However, a lower rate of TE (50 g ha−1) might be enough to minimize plant lodging without impairing the physiological quality of the seeds, depending on the rate of N fertilization. This study is the first step in providing empirical evidence for the detrimental effects of TE in combination with N on wheat seed quality, suggesting that seed producers should exercise caution in managing TE and N fertilization.