The EU aims to harmonise soil health monitoring across Member States with the Soil Monitoring Law. Selection of appropriate soil health indicators remains a key challenge, however. Total organic carbon (TOC) content, a key factor in soil health, may be related to indicators of microbial soil health. The aim of this study was to assess the relationship between various microbial soil health indicators and TOC in the topsoil of arable fields in Flanders (northern Belgium). Carbon (C) input from exogenous organic matter (C input) was also explored as a proxy for TOC. Four microbial soil health indicators were examined: (1) Hot-water extractable C (HWC), (2) Total biomass according to phospholipid fatty acid analysis (PLFA), (3) Bacterial (DivB) and (4) Fungal (DivF) Shannon-Wiener diversity. Five medium- to long-term field trials with different field histories and spatial variability were selected based on different C inputs. Results showed that both TOC and C input were good predictors for HWC and PLFA. A positive relationship between C input and TOC was found. This supports the use of C input as a practical proxy for monitoring TOC changes in soils (e.g., for carbon farming and soil health assessments). Significant within-field spatial variability was observed for TOC, HWC and PLFA, suggesting that spatial differences in soil health assessments should be addressed via sampling design. DNA-based indicators (DivB and DivF) were less influenced by spatial or management factors and also correlated weakly with TOC. These findings highlight the complex interplay among field history, current management and spatial variability when determining soil health.