Agroecological practices can be used to optimise ecological functions and improve the health of agroecosystems. The present study aimed to determine the effects of two agroecological systems (AG and AGSPP) on soil biodiversity and ecosystem services in tropical market gardens. The AG (agroecological) cropping system allows the use of organic phytosanitary products, unlike the second one (AGSPP, agroecological without phytosanitary products). The cropping systems were established in the open field and compared in terms of (i) soil fauna, (ii) soil fertility, (iii) soil aggregation, (iv) pest regulation, and (v) crop production. A total of eighteen months after the establishment of the experiment, the macrofaunal communities of the two cropping systems were significantly different. The AGSPP cropping system was characterised by a higher abundance of predators, a better soil structure, a higher tomato fruit set rate, and a lower pest proliferation. The increase in plant diversity and the non-use of phytosanitary products could modify the macrofaunal communities and, consequently, the provision of some ecosystem services. We also observed an effect of repellent and host plants on pest control in both systems, promoting high crop production. Overall, we showed that small changes in agroecological practices can have positive effects on soil biodiversity, pest regulation, and crop production.