Background Internally displaced persons fleeing their homes due to conflict and drought are particularly at risk of morbidity and mortality from diarrhoeal diseases. Regular handwashing with soap (HWWS) could substantially reduce the risk of these infections, but the behaviour is challenging to practice while living in resource-poor, informal settlements. To mitigate these challenges, humanitarian aid organisations distribute hygiene kits, including soap and handwashing infrastructure. Our study aimed to assess the effect of modified hygiene kits on handwashing behaviours among internally displaced persons in Moyale, Ethiopia. Methods The pilot study evaluated three interventions: providing liquid soap; scented soap bar; and the inclusion of a mirror in addition to the standard hygiene kit. The hygiene kits were distributed to four study arms. Three of the arms received one of the interventions in addition to the standard hygiene kit. Three to six weeks after distribution the change in behaviour and perceptions of the interventions were assessed through structured observations, surveys and focus group discussions. Results HWWS was rare at critical times for all study arms. In the liquid soap arm, HWWS was observed for only 20% of critical times. This result was not indicated significantly different from the control arm which had a prevalence of 17% (p-value = 0.348). In the mirror and scented soap bar intervention arms, HWWS prevalence was 11 and 10%, respectively. This was indicated to be significantly different from the control arm. Participants in the focus group discussions indicated that liquid soap, scented soap bar and the mirror made handwashing more desirable. In contrast, participants did not consider the soap bar normally distributed in hygiene kits as nice to use. Conclusion We found no evidence of an increased prevalence of handwashing with soap following distribution of the three modified hygiene kits. However, our study indicates the value in better understanding hygiene product preferences as this may contribute to increased acceptability and use among crisis-affected populations. The challenges of doing research in a conflict-affected region had considerable implications on this study’s design and implementation. Trial registration The trial was registered at www.ClinicalTrials.gov 6 September 2019 (reg no: NCT04078633).