Objective The objective of this study was to deliver an intervention to improve health awareness for infection prevention, hygiene, and sanitation to assess its impact. Furthermore, it aimed to identify the risk of multimorbidity in women of reproductive years from low socio-economic background. Methods A randomized control trial was conducted in Pakistan among women aged 15–45 years. Overall, 820 women participated in the baseline survey; 388 women were part of the control group and 360 of the intervention group. A digital health literacy intervention was delivered by 91 trained community health workers. Data were analyzed using descriptive statistics and multivariate logistic regression. Results About 35.9% of women suffered from multimorbidity. The intervention group showed higher odds of confidence in managing health with respect to skill and technique acquisition (AOR = 2.21; 95% CI 1.01–4.84), self-monitoring and insight (AOR = 2.97; 95% CI 1.29–6.80) as well as sanitation and hygiene (AOR = 1.42; 95% CI 1.07–1.93). Two primary outcomes related to hand hygiene and protective behavior against infection did not show any significant improvement. The secondary outcomes of the study related to impact on overall health-related quality of life, social integration and support, and emotional well-being also did not show any significant improvement. Conclusions Digital health literacy interventions and multimorbidity management for women of reproductive years at the primary level are a way forward to alleviate communicable and non-communicable disease burden in developing countries like Pakistan. These efforts are also critical to improve maternal and child health in developing regions.