Tropical wetlands significantly impact greenhouse gas (GHG) budgets and carbon storage: however data from sub-Saharan African (SSA) remain limited. Highland valley-bottom wetland (HVBW) agriculture supports millions, yet its effects on GHG emissions and carbon storage remain undocumented. This study quantified soil emissions of nitrous oxide (N₂O), carbon dioxide (CO₂), and methane (CH₄) in the Taita Hills, Kenya, from 12 converted, 10 recovering, and one reference (intact) HVBWs. Agricultural conversion shifted wetland emissions from CH₄ to N₂O dominance. Converted HVBWs were N₂O sources (2.7 kg N₂O–N ha⁻¹yr⁻¹), driven by elevated soil nitrate, whereas the intact wetland was an N₂O sink (−0.3 kg N₂O–N ha⁻¹ yr⁻¹), with high soil moisture and high soil C/NO₃⁻–N ratio suggesting complete denitrification. Recovering HVBWs showed intermediate N₂O emissions (0.6 kg N₂O–N ha⁻¹ yr⁻¹). CO₂ emissions were similar between converted and recovering HVBWs (10,850 vs. 11,031 kg CO₂–C ha⁻¹ yr⁻¹) but lower in the intact (2,923 kg CO₂–C ha⁻¹ yr⁻¹). CH₄ emissions were highest in the intact HVBW (2,757 kg CH₄–C ha⁻¹ yr⁻¹), intermediate in recovering sites (879 kg CH₄–C ha⁻¹ yr⁻¹), and lowest in converted sites (37 kg CH₄–C ha⁻¹ yr⁻¹). The intact HVBW had 224 Mg C ha⁻¹, indicating carbon loss rates of 2.6 Mg C ha⁻¹ yr⁻¹ over 45 years for converted HVBWs. Restoring Taita Hills wetlands would sequester 1.1 Mg C ha⁻¹ yr⁻¹, offsetting ~0.0005 % of Kenya's annual agricultural GHG emissions, or 9.8 % when scaled nationally. These findings highlight trade-offs between GHG emissions and carbon storage in HVBWs, with wetland recovery promoting functional restoration and long-term carbon sequestration in SSA.