In this work the presence and migration behavior of mycotoxins formed in sweet pepper, inoculated by Fusarium species involved in internal fruit rot, were investigated. Two different commercial sweet pepper cultivars were inoculated with two different Fusarium proliferatum isolates that were sampled from diseased peppers. After 10 days of incubation at 20 °C in a closed container, the lesion caused by the fungal infection was dissected. Around the lesion, up to three concentric rings of pepper fruit tissue with a width of 5 mm were cut out and analyzed using a multimycotoxin LC-MS/MS method. The analyses resulted in the detection of beauvericin and fumonisins B(1), B(2), and B(3). Beauvericin was detected only in the lesions (95%), and the levels varied between 67 and 73800 µg/kg. Fumonisins B(1), B(2), and B(3) were detected in the lesions and in the surrounding tissue, indicating migration of these toxins into healthy parts of the sweet pepper. In the lesion the fumonisin B(1) level varied between 690 and 104000 µg/kg. Even in the outer ring fumonisin B(1) was still present. Mostly it was present at a lower level than in the lesion, with a maximum level of 556 µg/kg. A similar migration behavior was obtained for fumonisins B(2) and B(3), but lower levels were detected in the lesions, up to 10900 and 1287 µg/kg, respectively. The analysis of 20 pepper samples resulted in the detection of beauvericin or alternariol. Seven samples were contaminated, and the level of beauvericin was 124 µg/kg (N = 1), whereas the level of alternariol varied from below the LOQ (6.6 µg/kg) to 101 µg/kg (N = 6).