Introduction: There is little iterature data regarding neutropenic enterocolitis (NE) development after autologous hematopoietic cell transplantation (auto-HCT) in non-Hodgkin lymphoma (NHL) patients. The aim of this study was to determine the incidence, risk factors, and clinical outcome of NE after auto-HCT in NHL patients with respect to the impact of multidrug-resistant Gram-negative bacteria (MDRG) and vancomycin-resistant enterococci colonization on the early outcome after auto-HCT. Material and methods: This retrospective single-center analysis included a total of 65 NHL patients who underwent auto-HCT after BEAM (BCNU, etoposide, cytosine arabinoside, melphalan) conditioning (BEAM-auto-HCT). Results: NE was diagnosed in nine (13.8%) patients, a median four days after auto-HCT. In 6/9 (66%) patients, septic shock following NE was diagnosed. In univariate analysis, MDRG colonization before BEAM-auto-HCT was the only factor significant for NE development [odds ratio (OR) 2.4 (1.14–5.0), p = 0.027], although this was not confirmed in multivariate analysis. Additionally, NE [OR 5.2 (1.9–13.9), p = 0.001] and MDRG colonization prior to transplant [OR 2.7 (1.0–7.0), p = 0.041] were independent factors for septic shock development. Conclusions: Our findings suggest that NHL patients presenting with MDRG colonization before transplant should be kept under careful surveillance because of the high risk of the development of early severe infectious complications, including abdominal ones.