Gender disparities are pronounced in Zomba district, Malawi. Among women aged 15–49 years, HIV prevalence is 16.8%, compared with 9.3% among men of the same age. Complex structural factors are associated with risky sexual behaviour leading to HIV infection. This study’s objective was to explore associations between multilevel measures of economic resources and women’s empowerment with risky sexual behaviour among young women in Zomba. Four measures of risky sexual behaviour were examined: ever had sex, condom use and two indices measuring age during sexual activity and partner history. Multilevel regression models and regression models with cluster-robust standard errors were used to estimate associations, stratified by school enrolment status. Among the schoolgirl stratum, the percentage of girls enrolled in school at the community level had protective associations with ever having sex (OR = 0.76; 95% CI: 0.60, 0.96) and condom use (OR = 1.06; 95% CI: 1.01, 1.11). Belief in the right to refuse sex was protective against ever having sex (OR = 0.76; 95% CI: 0.60, 0.96). Participants from households with no secondary school education had higher odds of ever having sex (OR = 1.59; 95% CI: 1.14, 2.22). Among the dropout stratum, participants who had not achieved a secondary school level of education had riskier Age Factor and Partner History Factor scores (β = 0.51; 95% CI: 0.23, 0.79, and β = 0.24; 95% CI: 0.07, 0.41, respectively). Participants from households without a secondary school level of education had riskier Age Factor scores (β = 0.26; 95% CI: 0.03, 0.48). Across strata, the most consistent variables associated with risky sexual behaviour were those related to education, including girl’s level of education, highest level of education of her household of origin and the community percentage of girls enrolled in school. These results suggest that programmes seeking to reduce risky sexual behaviour among young women in Malawi should consider the role of improving access to education at multiple levels.