Micro-nutrients are required in small amounts to maintain growth and cell functioning to complete the life cycle through reproductions. However, pregnant women in developing countries like Ethiopia are vulnerable to multiple micro-nutrient deficiencies. Therefore, this study aimed at assessing the serum level of metals and associated factors like dietary diversity, and health-related problems in pregnant women among small-scale farming in Kellem Wellega, western Ethiopia. A cross-sectional laboratory-based study was conducted from June to August 2021 on 417 pregnant women attending antenatal care at rural healthcare facilities. Data was collected by using per-tested structured questionnaires via face-to-face interviews. The data analysis was conducted using SPSS version 24.0, and multivariate logistic regression analysis was performed to determine the association between predictor and outcome variables. A statistically significant was considered at p value < 0.05 for all the analyses. Our study findings showed that 62.1, 80.9, and 71.9% of the participants were deficient in iron, zinc, and copper micro-nutrient levels, respectively. Pregnant women who could not have formal education were 3.24 (AOR = 3.24, 95% CI 1.33–7.91) and 3.98 (AOR = 3.98, 95% CI 1.2–13.15) times more likely to show zinc and copper deficiency than those who attended secondary school and above, respectively. Furthermore, pregnant women involved only in farming activities were 0.57 (AOR = 0.57, 95% CI 0.36–0.91) and 4.33 (AOR = 5.72, 95% CI 2.34–13.97) times more likely to be exposed to iron and zinc deficiency than those who were engaged in other activities. This study revealed that pregnant women with low income were 6.36 times more likely to be exposed to zinc micro-nutrient deficiencies than those with high-income participants (AOR = 6.36, 95% CI 1.47–27.61). Additionally, those participants who ate a varied diet between 1 and 4 items per day were 2.26 (AOR = 2.26, 95% CI 1.43–3.59) and 2.77 (AOR = 2.77, 95% CI 1.6–4.61) times more likely to suffer zinc and copper micro-nutrient insufficiency than those who consumed 5–10 items per day. Finally, pregnant women who developed diarrhea in the past three months were 1.82 (AOR = 2.77, 95% CI 1.14–2.92) and 2.52 (AOR = 2.52, 95% CI 1.3–4.91) times more likely to be exposed to iron and copper deficiency than those who never show the symptoms, respectively. This study identified low concentrations of zinc, iron, and copper in the blood serum of pregnant women of small-scale farmers.