Background: Optimal complementary feeding is critical for adequate growth and development in infants and young children. The associations between complementary feeding and growth have been studied well, but less is known about the relationship between complementary feeding and micronutrient status. Methods: Using data from a national cross-sectional survey conducted in Ghana in 2017, we examined how multiple WHO-recommended complementary feeding indicators relate to anemia and the micronutrient status of children aged 6–23 months. Results: In total, 42%, 38%, and 14% of the children met the criteria for minimum dietary diversity (MDD), minimum meal frequency (MMF), and minimum acceptable diet (MAD), respectively. In addition, 71% and 52% of the children consumed iron-rich foods and vitamin A-rich foods, respectively. The prevalence of anemia, iron deficiency (ID), iron deficiency anemia (IDA) and vitamin A deficiency (VAD) was 46%, 45%, 27%, and 10%, respectively. Inverse associations between MMF and socio-economic status were found, and MMF was associated with an increased risk of ID (55%; p < 0.013) and IDA (38%; p < 0.002). Conclusion: The pathways connecting complementary feeding and micronutrient status are complex. Findings related to MMF should be further investigated to ensure that complementary feeding programs account for the potential practice of frequent feeding with nutrient-poor foods.