Urogenital schistosomiasis (UGS) caused by zoonotic or hybrid schistosome infection(s) is an emerging public health concern in Malawi, and we describe a 1-year clinical sub-study with 3 inspection time points for female genital schistosomiasis (FGS) upon selecting 86 women with proven UGS. This sub-study was set within a broader 2-year longitudinal ‘Hybridization in UroGenital Schistosomiasis (HUGS)’ investigation. A detailed cervicovaginal examination with a portable colposcope was conducted, examining cervicovaginal lavage (CVL), cervical swab, cervical biopsy and urine with traditional parasitological and molecular diagnostic methods. At baseline, overt FGS by colposcopy was 72.1%, 64.3% by CVL real-time PCR and 51.2% by both colposcopy and CVL-PCR, noting urine-microscopy could often be negative. Human papillomavirus was detected in 31.0% of the cervical swabs, with 8.3% women also FGS positive by colposcopy and real-time PCR. Over the year, FGS prevalence by colposcopy increased by 32.7% during the study to 84.6%, homogenous yellow and grainy sandy patches being very common in the youngest 18–25 age group, where 51.9% were positive. FGS appears widespread locally and we discuss difficulties in its detection without invasive sampling. In addition to the presence of S. haematobium, S. mattheei was noted alongside key concurrent sexually transmitted infections. From our findings, we point out that improved prevention and management of FGS is required, foremost, better availability and regular accessibility to praziquantel treatment is needed. Furthermore, targeted health education, raised community awareness and dovetailing synergistic public health activities within Sexual and Reproductive Health services and local HIV/AIDS programmes could develop an appropriate holistic health intervention package.