Pulses get increasing awareness not only for their nutritional value but also for their multifunctionality in sustainable agri-food systems. Although having a long tradition in Mediterranean regions, their share of arable land is very low. Knowledge about pulse cropping, considering nonmarket outputs in alternative cropping systems, is scarce. To this end, we conducted a systematic literature research. We synthesized the current quantified state of knowledge about associated biodiversity in pulse systems and ecosystem services, specifically food/feed provision and soil quality, in lentil and chickpea cropping systems using alternative management practices in the Mediterranean and analysed their impact compared to conventional practices employing a meta-analysis. As alternative practices, we considered practices frequently proposed to be sustainable and more ecologically oriented than conventional cropping. Most studies examined soil quality, especially chemical quality, followed by grain yield. Very few studies surveyed biodiversity, most of which used arable flora as an indicator. Mean lentil and chickpea grain yields were 1484.4 ± 665 kg/ha under alternative practices, and flora richness was on average 10.9 ± 4 species during the pulse phase. We found significant positive impacts of organic farming on biodiversity, no tillage on soil quality and diversified rotations on yield. In multiservice trials, no tillage tended to be synergistic for both, yield and soil quality. In conclusion, organic and conservation agriculture elements seem promising techniques for ecosystem service-enhancing pulse management. Anyhow, the current evidence base on ecosystem service performance in alternative pulse systems is empirically not yet robust to conclude sound data-driven management recommendations—especially with a focus on biodiversity. However, we can draw justified hypotheses that can focus future research and can be tested in the field.