Background: Globally, anemia is a public health problem affecting the life of more than two billion people. Pregnant women are at high risk of iron deficiency anemia due to increased nutrient requirement during pregnancy. Iron-folic acid supplementation is the main strategy for prevention and control of iron deficiency anemia and its effectiveness depends on adherence to Iron-Folic Acid tablets. In the refugee camps of Ethiopia, despite the efforts made to reduce iron deficiency anemia during pregnancy, information about adherence to iron-folic acid supplementation and its associated factors are lacking. The objective of this study was to assess magnitude and factors associated with adherence to iron-folic acid supplementation, among pregnant women, in Shire refugee camps. Methods: Institution based cross-sectional study with mixed design (quantitative and qualitative) was carried out among pregnant women in Shire refugee camps from September to November 2015. For quantitative data, a sample of 320 pregnant women was systematically selected and data were collected via interview administered structured questionnaire. Quantitative data were coded and entered into Epi-info version 3.5.1 and exported into a statistical package for social sciences (SPSS) Version 19.0 software for analysis. Bivariable and multivariable logistic regressions were employed to identify the predictors at p-value the mean value were considered as somehow knowledgeable and those who scored ≤the mean value were considered as less knowledgeable. Data were coded and entered into Epi-info version 3.5.1 and exported into statistical package for social sciences (SPSS) Version 21.0 software for analyses. Descriptive statistics were employed to describe the study population in relation to socio-demographic and other relevant variables and to display findings in mean, median, percentage and 95% confidence intervals. A composite scale was constructed for maternal knowledge about anemia. To identify factors associated with adherence to IFA supplementation, first a bivariable logistic regression was performed for each independent variable with adherence to IFA supplementation and crude odds ratio with 95% confidence intervals was obtained. Subsequently, significant variables in the bivariable analysis (p-value < 0.2) were incorporated into the multivariable logistic regression to determine independent predictors of adherence to IFA supplementation among pregnant women. To control the effect of the four different health facilities (camps), a random effect was estimated using Generalized Estimating Equation (GEE) model. Results were summarized using tables, figures and graphs. The goodness of fit of the final logistic model was tested using Hosmer and Lemeshow test. For the knowledge-related questions, reliability was checked during pretest using Cronbach’s Alpha, which was 0.746. Open code version 3.6.2.0 software was used for analysis. Data were recorded by tape recorders from six FGDs and three KIIs were transcribed word-by-word into plain text and translated into English. After codes were developed, issues discussed and themes developed. The codes developed from the texts were coded into the following terms: availability of tablets, knowledge about IFA supplementation, attitude about IFAs, information from health professionals, and the perception of women, as they are healthy, parity and gravidity. The themes developed from the codes were personal factors, health facility-related factors, and pregnancy-related factors. All authors together develop the codes and themes of the qualitative data. An MSc expert in Health Education assisted how to analyze the qualitative data. Finally, the themes were triangulated with quantitative findings.