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Antimicrobial resistance is an increasing global problem and complicates successful treatments of bacterial infections in animals and humans. We conducted a longitudinal study in Mecklenburg-Western Pomerania to compare the occurrence of ESBL-producing <i>Escherichia</i> (<i>E.) coli</i> in three conventional and four organic pig farms. ESBL-positive <i>E. coli</i>, especially of the CTX-M type, were found in all fattening farms, confirming that antimicrobial resistance is widespread in pig fattening and affects both conventional and organic farms. The percentage of ESBL-positive pens was significantly higher on conventional (55.2%) than on organic farms (44.8%) with similar proportions of ESBL-positive pens on conventional farms (54.3–61.9%) and a wide variation (7.7–84.2%) on organic farms. Metadata suggest that the farms of origin, from which weaner pigs were purchased, had a major influence on the occurrence of ESBL-producing <i>E. coli</i> in the fattening farms. Resistance screening showed that the proportion of pens with multidrug-resistant <i>E. coli</i> was similar on conventional (28.6%) and organic (31.5%) farms. The study shows that ESBL-positive <i>E. coli</i> play a major role in pig production and that urgent action is needed to prevent their spread.