The objective of this two-year study was primarily the evaluation of the free and the bound forms of phenolic acids and phenolic aldehydes (PAAs) in grains of four selected cultivars of spring durum wheat subjected to three treatment intensities (GD—Green Deal, BT—Basic and IT—Intensive). All treatments included a common basic level and different spring production levels of nitrogen fertilisation (0 kg N in the case of GD; 30 kg N in the case of BT; and 60 kg N in the case of IT). Pesticide applications included herbicides and insecticides in both the BT and IT treatments, which were supplemented by combinations of fungicide and morphoregulator in the IT treatment. The GD treatment included only basic nitrogen, herbicide protection, and the application of a biostimulator (ExelGrow). The spring durum wheat cultivars subjected to testing were cultivated under Central European conditions, specifically in the Czech Republic’s central Bohemian region. UHPLC-ESI-MS/MS was used for the detection and accurate quantification of PAAs. In parallel, 12 other nutritional and basic technological parameters of the cereal were evaluated. Nine bound and seven free forms of PAAs were quantified in the analysed cereal samples. Bound forms of PAAs were dominant, accounting for 99.4% of total PAAs. Considering single PAAs, ferulic acid was the most abundant, accounting for 87% of the total bound PAAs. Interestingly, year and treatment intensity were the key factors in the variability of both free and bound PAAs, but these factors had different effects on bound PAAs. Under low nitrogen conditions, plants responded with an increase in free PAAs in particular, as well as in three bound PAAs. Unfavourable weather conditions, combined with the presence of biotic factors (e.g., Fusarium infections), significantly influenced the increase in both PAA groups, with the exception of free p-coumaric acid. PCA analysis confirmed close relationships between PAAs within both categories (free and bound). Subsequent correlation analysis further revealed that the immunoreactive gluten component (G12) exhibited a high negative correlation with the dominant ferulic acid (r = −0.70) and sinapic acid (r = −0.68). Additionally, moderate negative correlations were observed between four bound phenolic acids and grain hardness (r = −0.48–−0.60).