One of the challenges of sustainable horticulture is to preserve soil quality (SQ) by reducing the intensity of tillage operations and adopting practices that maintain soil organic matter (SOM). Relationships between best soil management practices, SOM fractions and soil health in organic and conventional vegetable production systems (VPS) are still unclear. This study aimed to evaluate the relationships between SOM fractions and biological indicators of SQ, looking for potential indicators of the impacts of best soil management practices (BMP) in VPS. Ninety soil samples were collected at 0-10 cm depth (48 organic and 42 conventional systems) from 53 vegetable producing areas in the Federal District, Brazil. The adoption level of each BMP was assessed by assigning scores ranging from 1 to 10. Total soil carbon determined by dry combustion (SOCDC), soil organic carbon by Walkley-Black method (SOCWB), particulate organic carbon (POC), potassium permanganate oxidizable carbon (POX-C), mineral-associated organic carbon (MOC), fulvic acids (FA) and humic acids (HA), humin (HU), fractions F1, F2, F3, F4, beta-glucosidase (GLU) and Arylsulfatase (ARYL) activity were determined. In the field, farmers answered a semi-structured questionnaire relating the management practices adopted in the VPS. ARYL activity levels, labile and stable fractions of SOM were higher in the samples from the organic areas than in the conventional ones, except for F3. ARYL showed moderate and strong correlations with POC, POX-C, F1, F2, HA, HU, SOCWB and SOCDC, while GLU correlated moderately only with POC and FA. According to a principal component analysis, the most differentiated organic and conventional VPS indicators were POC, POX-C, F1, F2, HA, HU, SOCWB, SOCDC and ARYL. According to PCA, no clear effect of the adoption time of the VPS on the soil organic and biological properties was observed. Organic systems can serve as a reference for the search for SQ in vegetable production as they maintain good relationships between organic matter fractions and SQ.