Introduction The Coronavirus Disease 2019 (COVID-19) pandemic has resulted in a major breakdown of health service provision in the fight against neglected tropical diseases (NTDs). COVID-19 may impact NTDs service delivery in varied ways. As the Ghana NTD programme planned to resume MDA activities, we examined the COVID-19 related perceptions and practices among some community members and frontline health workers for NTD control activities in the country. Methods The study was conducted in seven communities in the Ahanta West district of Ghana. This was a qualitative study using in-depth interviews (IDI) and focus group discussions (FGDs) for data collection. Participants were purposively selected from varied backgrounds to represent both beneficiaries and service providers directly involved in NTD programme implementation. Trained and experienced qualitative data collectors conducted the FGD and IDI sessions in the local Twi language, while health worker sessions were conducted in English. Discussions were audio-recorded and transcribed directly into English. Data was analysed using an iterative process. The transcripts were pre-coded using the broad themes, entered into a computer using Microsoft Word, and then imported into the MAXQDA software for thematic content analysis to select relevant representative narratives for presentation. Results Participants were aware of the COVID-19 pandemic and referred to it appropriately as ‘coronavirus’, COVID-19, and often as ‘the new disease’. Though many respondents could not describe the route of transmission, most of them reported that it is transmitted through touch or sharing of common items. They reported some signs/symptoms like fever, headache and difficulty breathing, and prevention methods like the use of hand sanitiser, washing of hands and sneezing appropriately. Respondents have reported that COVID-19 has negatively affected their daily lives by limiting their movements and therefore work. It also came to light that COVID-19 has also negatively affected the NTD programme implementation, especially mass drug administration (MDA) activities, leading to the postponement of the yearly MDA. The COVID-19 pandemic has negatively affected clinic attendance; people are afraid that they may be tested for COVID-19 at the clinic. Conclusion COVID-19 has negatively affected the NTD programme. Education and the provision of personal protective equipment will be required to build the confidence of frontline care providers including community drug distributors and community members in order to enhance quality service and participation in future MDA activities.