Livestock manure is applied to rangelands as an organic fertilizer to stimulate forage production, but the long‐term impacts of this practice on soil carbon (C) and greenhouse gas (GHG) dynamics are poorly known. We collected soil samples from manured and nonmanured fields on commercial dairies and found that manure amendments increased soil C stocks by 19.0 ± 7.3 Mg C ha⁻¹ and N stocks by 1.94 ± 0.63 Mg N ha⁻¹ compared to nonmanured fields (0–20 cm depth). Long‐term historical (1700–present) and future (present–2100) impacts of management on soil C and N dynamics, net primary productivity (NPP), and GHG emissions were modeled with DayCent. Modeled total soil C and N stocks increased with the onset of dairying. Nitrous oxide (N₂O) emissions also increased by ~2 kg N₂O‐N ha⁻¹ yr⁻¹. These emissions were proportional to total N additions and offset 75–100% of soil C sequestration. All fields were small net methane (CH₄) sinks, averaging −4.7 ± 1.2 kg CH₄‐C ha⁻¹ yr⁻¹. Overall, manured fields were net GHG sinks between 1954 and 2011 (−0.74 ± 0.73 Mg CO₂ e ha⁻¹ yr⁻¹, CO₂e are carbon dioxide equivalents), whereas nonmanured fields varied around zero. Future soil C pools stabilized 40–60 years faster in manured fields than nonmanured fields, at which point manured fields were significantly larger sources than nonmanured fields (1.45 ± 0.52 Mg CO₂e ha⁻¹ yr⁻¹ and 0.51 ± 0.60 Mg CO₂e ha⁻¹ yr⁻¹, respectively). Modeling also revealed a large background loss of soil C from the passive soil pool associated with the shift from perennial to annual grasses, equivalent to 29.4 ± 1.47 Tg CO₂e in California between 1820 and 2011. Manure applications increased NPP and soil C storage, but plant community changes and GHG emissions decreased, and eventually eliminated, the net climate benefit of this practice.