The intensification of the agricultural practices in Europe over the last decades has drastically transformed the agroecosystems. The simplification of the landscape, the loss of semi-natural habitats and the application of chemicals on crops led to biodiversity decline in agricultural landscapes, raising substantial concerns about the loss of essential ecosystem services, such as pollination or pest control. Depending on the location, the scale and the regional context, different indicator species groups (ISGs) are regularly surveyed to assess the state and trend of biodiversity changes in agroecosystems. Although the high diversity of these ISGs allows assessing different biodiversity aspects (e.g., trophic levels, bio-physical compartments, scale of indication), it complicates the interpretation of the results and thus their practical application. In addition, species diversity metrics are various, from simple species counts to more complex measurements of diversity indices, sometimes with antagonistic responses. Here, to meet the pressing need for synthesis in this complex topic, we follow a standardized systematic map protocol to collect and summarize the literature reporting field evidence of the effects of the main agricultural management practices (AMPs) in arable crops, grasslands and ecological infrastructures on a set of ISGs in European lowland farming areas. Searches of literature were made using online publication databases, search engine and specialist websites in English. Gathered publications were screened for relevance following inclusion/exclusion criteria published in a prior protocol. We extracted and mapped information about experimental design, monitoring methods, ISGs and AMPs studied and the diversity measures presented in each included publication. These parameters are structured in available data coding sheets. The search gathered 20,162 references from which 1208 remained after full text eligibility screening. Main areas studied are in Western Europe, and the number of studies increased exponentially from 1984 to 2022. Most publications are experimental and on-farm studies which assess AMPs effects at the field scale. Main studied AMPs are fertilization, grazing, organic farming, tillage, mowing and herbicide application. Most ISGs used to study their impacts are flora, carabids, spiders, birds, bees and annelids, often combined with other ISGs. The combinations between AMPs and ISGs studied are detailed as well as monitoring methods. The most used diversity measures are abundance, species richness, Shannon index, evenness, and community composition. We identified several knowledge clusters: (1) organic farming, fertilization, tillage, grazing and mowing impact on a wide range of ISGs, (2) flora response to agricultural practices, (3) annelids response to agronomic interventions that impact soil structure (e.g., tillage, fertilization, crop rotation, crop residue management), (4) butterflies and orthopterans response to mowing and grazing effects in grasslands, (5) the use of bird monitoring for the impact for assessing the efficiency of AES implementation at the landscape scale. We highlight that further research should be conducted on ISGs that are until now poorly studied regarding agricultural practices, such as amphibians, reptiles, gastropods, millipedes and centipedes. More field evidence of the effects of diversification practices such as intercropping, undersowing, intermediate cropping, and agroforestry are needed to draw conclusions on their benefits on biodiversity. The online version contains supplementary material available at 10.1186/s13750-024-00347-0.