Background Lymphatic filariasis (LF) is endemic in Ghana, and the country has implemented the GPELF strategy since 2000 with significant progress made in the control of the disease. However, after several years of mass drug administration (MDA) implementation, there is persistent transmission in 17 of the 98 endemic districts in the country. Current approaches to surveillance are clearly unable to target untreated individuals and new strategies are required to address the endgame challenges to enhance LF elimination as a public health problem in endemic countries. Community registers are used during MDAs to enumerate community members, their age, gender, house numbers, and records of their participation in MDAs. These MDA registers represent an untapped opportunity to identify and characterize non-compliance and inform appropriate programmatic actions. In this study, we analyzed the data presented in the registers to assess the coverage and individuals’ compliance in MDA. Methods The information in the MDA registers were assessed to verify the reported coverages obtained from the district. The community registers were obtained from the district health offices and the data from each individual record was entered into a database. A simple questionnaire was used to cross-check the participation of study participants in the 2017 MDA. The questionnaire solicited data on: participation in the 2017 MDA, reasons for not taking part in the MDA, adverse events experienced, what was done for the adverse events, and willingness to participate in subsequent MDAs. Results We found that 40.1% of the population in the registers missed at least one MDA in 3 years (2016–2018) and the majority of them were between 10–30 years of age. The results of the questionnaire assessment indicated that 13.8% of the respondents did not receive treatment in 2017 for various reasons, the most prominent among them being “absence/travel” (37.1%). Data in the registers were used to verify the treatment coverage for the years 2017 and 2018, and reviewed against the reported coverage obtained from the district. Significant differences between the reported and verified coverages were only observed in four communities. However, the assessment also revealed that the reported coverage was only accurate in 33.3% of cases. Conclusions The MDA registers allow for the identification of eligible individuals who were not reached during any MDA round. Thus, the MDA registers could be utilized at the community and programme levels to identify missing and untreated individuals, appropriately address their non-compliance to MDA, and thereby improve MDA coverage in each implementation unit and monitor the progress towards elimination of LF. The challenges observed through the review of the registers also offer opportunities to improve the training given to the community drug distributors., Author summary Elephantiasis is a disease that is common in Ghana. Since the year 2000 the country has implemented a control programme aimed at eliminating the disease as a public health problem, through the yearly treatment of entire communities in districts where the disease is found. Achievements have been made, and treatment has stopped in many districts; however, some districts have received many years of treatment without successfully reducing the infections below the targeted levels. Many individuals go untreated every year, as can be observed from the low reported treatment coverage after MDA. This untreated population may explain why some districts have failed to achieve the criteria for stopping treatment. Fortunately, the treatments are recorded in community registers, which contain the details of all community members, as well as their treatment participation. These registers can therefore be used to identify people who have not received treatment and design appropriate interventions to reach them. Through these registers, we were able to identify and characterize individuals who were not treated between 2016 and 2018 in 10 communities. We found that 4 out of 10 people missed at least one treatment between 2016 and 2018, and the majority of them were 10–30 years of age. Using the information from the registers we were also able to verify the proportion of people who took part in the treatments in 2017 and 2018, and compared this to what was reported. This comparison revealed that the reporting was only accurate in 33% of cases. A questionnaire was also used to cross-check the participation of study participants in the 2017 MDA, with results indicating that 13.8% of the respondents did not receive treatment for various reasons, the most prominent among them being “absence/travel” (37.1%). Although these registers are seldom used by the Lymphatic Filariasis Control Programme for anything other than recording and reporting treatment information, this study shows that the registers provide an opportunity to identify individuals who have not received treatment, develop a plan to appropriately address their reasons for not taking part in the treatments, target these untreated individuals to improve the overall proportion of people taking part in MDA, and assess the accuracy of reported coverage information. These activities will allow the programme to better monitor the progress towards, and ultimately achieve, elimination of lymphatic filariasis as a public health problem.