(1) Elevated atmospheric CO2 (eCO2) may affect organic inputs to woodland soils with potential consequences for C dynamics and associated aggregation; (2) The Bangor Free Air Concentration Enrichment experiment compared ambient (330 ppmv) and elevated (550 ppmv) CO2 regimes over four growing seasons (2005–2008) under Alnus glutinosa, Betula pendula and Fagus sylvatica. Litter from the experiment (autumn 2008) and Lumbricus terrestris were added to mesocosm soils. Microbial properties and aggregate stability were investigated in soil and earthworm casts. Soils taken from the field experiment in spring 2009 were also investigated; (3) eCO2 litter had lower N and higher C:N ratios. F. sylvatica and B. pendula litter had lower N and P than A. glutinosa; F. sylvatica had higher cellulose. In mesocosms, eCO2 litter decreased respiration, mineralization constant (respired C:total organic C) and soluble carbon in soil but not earthworm casts; microbial‐C and fungal hyphal length differed by species (A. glutinosa = B. pendula > F. sylvatica) not CO2 regime. eCO2 increased respiration in field aggregates but increased stability only under F. sylvatica; (4) Lower litter quality under eCO2 may restrict its initial decomposition, affecting C stabilization in aggregates. Later resistant materials may support microbial activity and increase aggregate stability. In woodland, C and soil aggregation dynamics may alter under eCO2, but outcomes may be influenced by tree species and earthworm activity.