Repeated applications of liquid dairy manure (LDM) and perennial crops generally favor nitrogen (N) stocks in soils, but in ways that may differ with soil type and other management practices. The objective of this study was to assess the long-term (21 yr) changes in soil N stocks (0–50 cm) of a silty clay soil, in a cool humid climate, in response to mineral fertilization (MIN) or LDM, combined with two tillage practices [chisel plow (CP), or moldboard plow (MP)], and two crop rotations [cereal monoculture (monoculture) or cereal–perennial forage rotation (forage-based rotation)]. The forage-based rotation favoured a greater accumulation of N in the first 20 cm of soil (+50 kg N·ha⁻¹·yr⁻¹) when compared with the monoculture. Tillage practices did not impact N stocks in the whole soil profile, but influenced its vertical distribution, with greater accumulation at the surface with CP, and at depth with MP. Annual input of LDM increased N stocks at the surface (0–20 cm) compared with MIN, especially when combined with the forage-based rotation. After 21 yr, soil N stocks (0–50 cm) with LDM were 32% (+2 t N·ha⁻¹) higher in the forage-based rotation than in the monoculture, suggesting better retention and more efficient use of manure-N with perennial forages than cereals. Comparisons between the N mass balance computed for each cropping system, and the changes in soil N stocks indicated that accumulation of N under the forage-based rotation was largely due to symbiotic fixation by legumes in the forage mixture.