Soil particle aggregation and its stability are vital for maintaining soil health, ecosystem functioning, and sustainable land use largely governed by soil organic carbon (SOC). However, long-term strategies to enhance aggregation and carbon sequestration in naturally acidic soils remain insufficiently explored. This study presents a rare long-term field experiment, initiated in 1949 on Retisol (moraine loam) in western Lithuania, to evaluate the effects of liming, farmyard manure (FYM), and their combination on soil aggregation and carbon dynamics. Treatments included (T₁) Unlimed and Unfertilized (Control), (T₂) FYM at 60 t ha⁻¹, (T₃) lime at 3.5 t ha⁻¹, and (T₄) lime + FYM. Amendments were applied every five years. Soil samples from depths of 0 to 10 cm and 10 to 20 cm were analyzed for aggregate distribution via dry (nine fractions) and wet sieving (five fractions), and classified into macroaggregates, mesoaggregates, microaggregates, and silt-clay fractions. Mean weight diameter (MWD), water-stable aggregates (WSA ≥ 0.25 mm), and carbon fractions [SOC, permanganate oxidizable carbon (POXC), humic and fulvic acids] were measured. The combined application of lime and FYM (T₄) significantly improved soil structure, increasing macroaggregates by 32.81%, while reducing mesoaggregates (−21.47%), microaggregates (−34.70%), and the silt-clay fraction (−33.15%) relative to the control. T₄ also showed the highest WSA (18.59%) and MWD (22.30%), followed by T₃ (13.48% WSA, 12.60% MWD) and T₂ (10.29% WSA, 5.60% MWD). SOC was highest in T4, particularly in the silt-clay fraction (19.28% higher than T₁). POXC was highest in mesoaggregates (57%) and the silt-clay fraction (46%), while fulvic acid content decreased by 35% in the silt-clay fraction under T_4. These findings provide novel, long-term evidence that the integration of lime with organic amendments enhances soil physical structure and promotes aggregate-associated carbon stabilization in acidic soils offering a sustainable and climate-resilient soil management strategy.