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Improving agricultural soil quality in semi-arid regions is necessary for reducing soil erosion and improving water use. Conservation agriculture (CA) can increase soil quality and biodiversity, and reduce operational costs without losing crop productivity both under irrigated or rainfed conditions. However, few studies on soil chemical and biochemical status in irrigated farms under CA in the Mediterranean region are available. Permanent beds with crop residue retention (PB) have been proposed as an alternative to conventionally tilled beds with residue incorporation into the soil (CB). These two soil management systems combined with controlled traffic were compared during two different seasons (2009 and 2010) in a loamy alluvial Typic Xerofluvent soil under a maize (Zea mais L)-cotton (Gossypium hirsutum L) crop rotation trial established in 2007 in Southern Spain. Total organic carbon (TOC), water soluble carbon (WSC), Kjeldahl nitrogen (Kjel-N), dehydrogenase (DHA) and p-glucosidase (beta-Glu) activities and microbial biomass carbon (MBC) and nitrogen (MBN) were analysed in soil from beds and furrows after crop harvest. Results indicated that Kjel-N, TOC and enzymatic activities were significantly higher in soil from furrows in PB than in CB, but practically no differences were found in soil from the bed zone. Moreover, traffic did not affect chemical and biochemical parameters in spite of its compacting effect. Major differences were found between samplings due to different quantity and nature of the residues (maize vs. cotton). Principal component analysis confirmed that TOC, Kjel-N and beta-Glu (and DHA to a less extend) are useful indicators of soil management impact on soil quality in this irrigated Mediterranean conditions; however, this is not the case of WSC, a common indicator in rainfed conditions. Results confirmed that conservation agriculture is the better option to increase soil biological and biochemical quality in irrigated farms under Mediterranean semi-arid conditions. (C) 2013 Elsevier B.V. All rights reserved.