Background: Infected pancreatic necrosis (IPN) is a serious complication of moderate-to-severe acute pancreatitis (AP), associated with high morbidity, intensive care unit (ICU) admission, organ failure, and mortality. Initial management relies on antibiotics and drainage of walled-off necrosis (WON). In the context of increasing multidrug-resistant (MDR) bacteria, identifying risk factors for MDR emergence is crucial. The impact of fungal infections (FIs) on outcomes also remains unclear. This study aimed to identify risk factors associated with the emergence of MDR bacteria and FIs during intervention for IPN. Methods: This retrospective study included 71 consecutive patients undergoing intervention for suspected IPN or symptomatic WON. Results: At first intervention, IPN was confirmed in 52 patients (73%), MDR bacteria in 19 (27%), extensively drug-resistant (XDR) bacteria in 4 (5.6%), and FI in 21 (30%). After all interventions, MDR/XDR bacteria and fungi were detected in 25 (35%)/11 (15.5%) and 42 (59%) patients, respectively. Independent risk factors for MDR emergence were the number of antibiotic changes (b, 1.70; 95% CI 1.18–2.43; p = 0.004) and need for nutritional support (NS) (b, 5.69; 95% CI 1.52–20.50; p = 0.010). No independent factor was associated with FI. The 180-day mortality did not differ across groups. The 90-day cumulative ICU admission rate was higher in IPN vs. non-IPN (63.1% vs. 29.4%, p = 0.030) and in MDR vs. non-MDR (72.2% vs. 37.1%, p = 0.005). Conclusions: Antibiotic changes and NS were independently associated with MDR emergence in IPN. No independent factors were linked to FI. ICU admission was significantly higher in IPN and MDR cases.