Antimicrobial resistance (AMR) is a global threat in humans and animals, and antimicrobial usage (AMU) has been identified as a main trigger of AMR. The purpose of this work was to compare data on AMR in clinical and non-clinical isolates of Escherichia coli in German broilers and turkeys between 2014 and 2017. Furthermore, we investigated AMR changes over time and the association of changes in AMU with changes in AMR. Data on clinical and non-clinical isolates together with data on therapy frequency of broilers and turkeys were collected from German monitoring systems. Logistic regression analyses were performed to assess the association between the explanatory factors (AMU, year and isolate type) and the dependent variable (AMR). In broilers, the analysis showed lower resistance proportions of clinical isolates of E. coli to ampicillin and colistin (ampicillin: Odds ratio (OR) and 95% confidence interval (CI) = 0.44 (0.3-0.64), p<0.001; colistin: OR and 95% CI = 0.75 (0.73-0.76), p<0.001) but higher proportions for cefotaxime (OR and 95% CI = 4.58 (1.56-15.1), p = 0.007). Resistance to ampicillin, gentamicin and tetracycline was less frequent in clinical isolates in turkeys (ampicillin: OR and 95% CI = 0.4 (0.29-0.53), p<0.001; gentamicin: OR and 95% CI = 0.5 (0.26-0.94), p = 0.035; tetracycline: OR and 95% CI = 0.4 (0.29-0.55), p<0.001). The analysis found decreasing associations of AMU with resistance to tetracycline in turkeys and to colistin in broilers. Year was associated with a decrease in resistance to colistin in broilers and to tetracycline in turkeys. Differences in resistance found in this study between clinical and non-clinical isolates might play an important role in resistance prevalence. This study indicated that further data analyses over longer time intervals are required to clarify the differences found between clinical and non-clinical isolates and to assess the long-term effects of changes in AMU on the prevalence of AMR.