Background: Allergic rhinitis (AR) is a chronic condition that affects children’s quality of life. Studies show that adding bacterial lysates (BLs) to treatment can improve outcomes, but their effects on the immune system are still not fully understood. Objectives: This study aimed to evaluate the immunomodulatory impact of sublingually administered polyvalent mechanical BL (PMBL) on the expression of T helper (Th) cell-associated transcription factors and cytokines in children with grass pollen-induced AR. Methods: Immunological analyses were performed on blood samples collected during a previously conducted randomised, double-blind, placebo-controlled clinical trial (NCT04802616). Children aged 5–17 years with grass pollen-induced AR received either sublingual PMBL or placebo in three 10-day treatment cycles, each followed by a 20-day break. Peripheral blood mononuclear cells were collected at baseline before the grass pollen season (V1) and after completion of the study treatment during natural peak pollen exposure (V2) and analysed by flow cytometry to assess the expression of transcription factors and cytokines associated with Th1, Th2, Th10, Th17, and Treg-like immune responses. Results: In the PMBL group, there was a significant increase in the expression of T-bet, E4BP4, FoxP3, IFN-γ, and IL-10, along with a reduction in GATA3 and IL-4 expression (p < 0.001). The placebo group exhibited increased expression of GATA3 (p < 0.001), RORγT (p < 0.001), and IL-4 (p = 0.004) and a reduction in T-bet expression (p = 0.007). Between-group comparisons at V2 revealed significantly higher expression of Th1-, Th10-, and Treg-associated markers, and lower Th2- and Th17-associated markers in the PMBL group compared to placebo. Conclusions: Sublingual PMBL administration modulates the expression of Th cell-associated transcription factors and cytokines in children with grass pollen-induced AR, consistent with enhanced Th1-, Th10-, and Treg-like immune responses and reduced Th2-associated activity.