Peru has one of the highest informal employment rates in Latin America (73%). Previous studies have shown a higher prevalence of poor self-perceived health (P-SPH) in informal than in formal workers. The aim of this study was to analyze the role of working conditions in the association between informality and SPH in an urban working population in Peru. We conducted a cross-sectional study based on 3098 workers participating in the working conditions survey of Peru 2017. The prevalence of P-SPH and exposure to poor working conditions were calculated separately for formal and informal employment and were stratified by sex. Poisson regression models were used to assess the association between P-SPH and informal employment, with crude and adjusted prevalence ratios (PR) for working conditions. Informal employment affected 76% of women and 66% of men. Informal workers reported higher exposition to poor working conditions than formal workers and reported worse SPH. Informal workers had a higher risk of P-SPH than formal workers: PR 1.38 [95% CI: 1.16–1.64] in women and PR 1.27 [95% CI: 1.08–1.49] in men. Adjustment by working conditions weakened the association in both sexes. In women, this association was only partially explained by worse working conditions; PR 1.23 [95% CI: 1.04–1.46]. Although some of the negative effect of informal employment on workers´ health can be explained by the characteristics of informality per se, such as poverty, a substantial part of this effect can be explained by poor working conditions.