Background: There are difficulties in carrying out research in low-income urban communities, but the methodological challenges and suggestions on how to deal with them are often undocumented. The aims of this study are to describe the challenges of recruiting and enrolling low-income pregnant women with periodontitis to a clinical trial on vitamin D/calcium milk fortification and periodontal therapy and also to describe the patient-, study protocol- and setting-related factors related to women's ineligibility and refusal to participate in the study. Methods: A mixed-method sequential exploratory design was applied. Qualitative and quantitative data on recruitment to a 2 × 2 factorial feasibility clinical trial were used. Eighteen women attending the health centre in a low-income area in Duque de Caxias (Rio de Janeiro, Brazil) took part in focus group discussions, and the data were thematically analysed. Quantitative data were analysed using appropriate descriptive statistics, including absolute and relative frequencies. Results: Of all referrals (767), 548 (78.5%) did not meet the initial eligibility criteria. The main reason for exclusion (58%) was advanced gestational age (> 20 weeks) at first prenatal appointment. In the periodontal examination (dental screen), the main reason for exclusion was the presence of extensive caries (64 out of 127 exclusions). Non-participation of those eligible after the periodontal examination was approximately 24% (22 out 92 eligible women) and predominantly associated with patient-related barriers (e.g. transportation barriers, family obligations, patients being unresponsive to phone calls and disconnected telephones). The study recruited 70 women with periodontitis in 53 weeks and did not reach the benchmark of 120 women in 36 weeks (58.3% of the original target). Recruitment was severely hindered by health centre closures due to general strikes. The recruitment yields were 9.1% (70/767) of all women contacted at first prenatal visit and 76.1% (70/92) of those screened eligible and enrolled in the trial. Women did not report concerns regarding random allocation and considered fortified milk as a healthful and safe food for pregnant women. Some women reported that financial constraints (e.g. transportation costs) could hinder participation in the study. Conclusion: Engagement between the research team and health centre staff (e.g. nurses) facilitated referral and recruitment, yet some pregnant women failed to participate in the study largely due to significant patient-related sociodemographic barriers and setting-related factors. Our data illustrate the complexity of overcoming recruitment and enrolment challenges for clinical trials in resource-limited settings. Trial registration: ClinicalTrials.gov, NCT03148483. Registered on 11 May 2017.