1. Cutover peatlands cover large surfaces of high potential value for biodiversity and carbon sequestration function if successfully restored but the evaluation of restoration success is not straighforward. We assessed the bioindicator value of organic matter (OM), testate amoebae (protozoa) and bacteria in peat from two regeneration stages and a reference site of a cutover bog. 2. Contrasting biochemical signatures of peat OM were observed along the regenerating profiles allowing clear differentiation between the newly regenerated peat and the old peat. Where peat macrofossils were absent sugar biomarkers allowed to infer peat botanical origin and OM alteration. 3. Over the succession, the OM composition of the new peat differed: peat from the recent stage was more dominated by Sphagnum-derived tissues and was characterised by lesser carbohydrate preservation and higher bacterial biomass than the advanced regeneration stage. 4. Surface testate amoeba communities also changed from the recent to the advanced stages of regeneration indicating a shift from wet and moderately acidic conditions to drier and more acidic conditions. Over this regeneration sequence (i) biomass and average size of species declined but were higher in the unexploited site (ii) species richness and diversity increased but density declined. 5. Synthesis and applications. Although the secondary succession in the cutover bog leads to an ecosystem similar to that of the reference site in terms of surface vegetation, OM and testate amoebae continue to reflect disturbances associated with peat harvesting. Nevertheless, the described dynamics of both microbial and biochemical variables over the succession showed similarities between the advanced stage and the reference: a higher testate amoeba diversity is associated with better carbohydrate preservation and a more heterogeneous botanical composition of the peat. The quantitative inference of water table depth and pH based on testate amoebae indicators represents an alternative to labour-intensive repeated measurements in the field. Botanical and biochemical composition of peat OM provides additional information on past anthropogenic perturbations of the bog and can be used for restoration monitoring. The combination of several indicators therefore provides a more complete assessment of ecological conditions which could be valuable for the management of cutover peatlands.