Equine-assisted intervention (EAI) studies deal with clients, whereas very few studies focused on the effects on animals. EAI equids are also submitted to management, which influences their welfare. Management and working conditions depend on human decisions and perception. We gathered information through a survey about facilities managers’ strategies (n = 51) and obtained direct information on management and working practices and their consequences on equids’ welfare through an observational study (n = eight facilities, 174 equids). Differences in managers’ perceptions of good management practices were related to the facility’s involvement in EAI, e.g., increased awareness of equids’ needs (housing and feeding), especially when EAI was the main activity. A detailed observational study on eight additional facilities confirmed that. Facility management profiles were paralleled by equids’ welfare profiles. Clear correlates were found between management decisions and welfare consequences. One major factor influencing welfare and human–equid interactions appeared to be working modalities, with more EAI facilities practicing groundwork and bitless work. Facilities where equids were the most involved in mixed activities had the most equids with compromised welfare. Given EAI clients’ particularities, conventional working modalities are less adapted and at risk of increased discomfort for equids. Overall, survey and observational approaches converged but some discrepancies (choice of equid type) appeared between the reported and observed prevalence.