There is increasing acceptance that children are not unaware of when they are targets of discrimination. However, discrimination as a consequence of socio-economic disadvantage remains understudied. The aim of this study was to examine the impact of perceived discrimination on well-being, perceptions of safety and school integration amongst children growing up within socio-economically disadvantaged communities in Limerick, Ireland. Mediation analysis was used to explore these relationships and to examine the potential role of parental support and community identity in boys and girls in the 6th to 9th year of compulsory education (N = 199). Results indicate perceived discrimination contributed to negative outcomes in terms of school integration, perceptions of safety and levels of well-being. Age and gender differences were observed which disadvantaged boys and younger children. All negative outcomes were buffered by parental support. Community identity also protected young people in terms of feelings of school integration and risk but not in terms of psychological well-being. Findings are discussed in terms of the different role of family and community supports for children negotiating negative social representations of their community.