Background: Globally, very limited studies have explored the unique contributions of hygiene and sanitation practices on the odds for stunting and underweight in children. Hence, the study examined the relationship between environmental hygiene and sanitation practices and odds for stunting and underweight among children under-five years old in rural communities in Ghana. Methods: The study was a cross-sectional study, in which study participants were simple randomly selected. All data were gathered from face-to-face interviews and by the use of observational checklist. Data were analysed using statistical product and service solutions software version 21.0. Further, binary logistics regressions model was used to assessed for adjusted odds of stunting and underweight across hygiene and sanitation practice variables. Results: Upon adjustment for the effects of covariates, children from households with toilet facilities had lower odds for underweight compared with their counterparts recruited from households without toilet facility [0.2(0.0-0.8); p = 0.031]. Also, lower frequency (1-3 times a week) of cleaning toilet facility per week was associated with higher odds for underweight compared with the higher frequency of cleaning (4 times or more per week) of toilet facility [4.5(1.3-15.3); p = 0.018]. Conclusions: The study revealed that both stunting and underweight were prevalent among the children. Also, inappropriate sanitation and hygiene practices were associated with increased odds for child malnutrition. The district health administration and the district assembly ought to intensify education on the importance of kitchen hygiene and the need for households to own toilet facilities.