Fasting period and fasting status affect the feeding practices and nutritional status of Ethiopian Orthodox mothers. Even if children are exempted from fasting, some mothers do not prepare their food from animal sources as it could contaminate utensils for cooking family foods. Therefore, the objective of this study was to assess feeding practices and undernutrition in 6–23-months old children whose mothers are Ethiopian Orthodox religion followers during lent fasting and non-fasting periods in rural Tigray, Northern Ethiopia, and to identify associated factors. A community-based longitudinal study was carried out in Ethiopian Orthodox lent fasting and non-fasting periods. Using a multi-stage systematic random sampling technique, 567 and 522 children aged 6–23 months old participated in the fasting and non-fasting assessments, respectively. Statistical analyses were done using logistic regression, an independent sample t-test, Wilcoxon signed-rank (WSRT) and McNemar’s tests. The prevalences of stunting, underweight and wasting were 31.6–33.7%, 11.7–15.7% and 4.4–4.8%, respectively. The weight-for-height (WHZ) and height-for-age (HAZ) values for children of fasting mothers were significantly lower (p < 0.05) compared to those of non-fasting mothers. Likewise, the median weight-for-age (WAZ) and diet diversity score (DDS) of children of fasting mothers were also significantly higher in non-fasting than in fasting periods. A small proportion of children (2.3–6.7%) met the minimum acceptable diet (MAD) in the study population, but these measures were significantly increased (p < 0.001) in the children of non-fasting mothers. Mother’s fasting during lactation period of the indexed child was amongst the independent factors common in child stunting, underweight and wasting. Nutritional status and feeding practices of 6–23-month-old children are affected by maternal fasting during the fasting period. Therefore, without involvement of religious institutions in the existing nutritional activities, reduction of undernutrition would not be successful and sustainable.