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Land management in tropical woodlands is being used to sequester carbon (C), alleviate poverty and protect biodiversity, among other benefits. Our objective was to determine how slash-and-burn agriculture affected vegetation and soil C stocks and biodiversity on an area of miombo woodland in Mozambique, and how C stocks and biodiversity responded once agriculture was abandoned. We sampled twenty-eight 0.125 ha plots that had previously been cleared for subsistence agriculture and had been left to re-grow for 2 to ~25 years, and fourteen 0.25 ha plots of protected woodlands, recording stem diameter distributions and species, collecting wood for density determination, and soil from 0 to 0.3 m for determination of %C and bulk density. Clearance for agriculture reduced stem wood C stocks by 19.0 t C ha-1. There were significant relationships between period of re-growth and basal area, stem numbers and stem biomass. During re-growth, wood C stocks accumulated at 0.7 t C ha-1 year-1. There was no significant difference in stem C stocks on woodlands and on abandoned farmland 20-30 years old. Soil C stocks in the top 0.3 m on abandoned land had a narrower range (21-74 t C ha-1) than stocks in woodland soils (18-140 t C ha-1). There was no discernible increase in soil C stocks with period of re-growth, suggesting that the rate of accumulation of organic matter in these soils was very slow. The re-growing plots did not contain the defining miombo species, and total stem numbers were significantly greater than in woodland plots, but species richness and diversity were similar in older abandonments and miombo woodlands. Wood C stocks on abandoned farmland were capable of recovery within 2-3 decades, but soil C stocks did not change on this time-scale. Woodland soils were capable of storing >100 t C ha-1, whereas no soil on a re-growing area exceeded 74 t C ha-1, so there is a potential for C sequestration in soils on abandoned farmland. Management should focus on identifying C-rich soils, conserving remaining woodlands to protect soil C and preserve defining miombo species, and on investigating whether fire control on recovering woodland can stimulate accumulation of soil C and greater tree biomass, and restore defining miombo species.