Background/Objectives: Vaccination is a strategy in pig farming for the control of several pathogens, but commercial vaccines may have detrimental side effects. This study aimed to evaluate the effects of commercial vaccines on the control of porcine circovirus type 2 (PCV2), Mycoplasma hyopneumoniae (Mhp), and Lawsonia intracellularis (L. intracellularis) and their potential side effects on welfare, behavior, acute inflammation biomarkers (C-reactive protein and haptoglobin), and the performance of piglets during the nursery phase. Methods: A total of 240 piglets, both female and castrated males, with an average weight of 6.3 ± 0.9 kg were subjected to four treatments: T1-FLEXcombo® (Ingelvac®CircoFLEX and Ingelvac®MycoFLEX) + Enterisol® Ileitis; T2-FLEXCombo® + Porcilis® Ileitis; T3-Porcilis® PCV M HYO + Porcilis® Ileitis; and T4-FLEXCombo® + 0.9% saline solution. This study measured therapeutic interventions, body condition score, behavioral changes, rectal temperature, and inflammation biomarkers post-vaccination. Results: The T3 group required more therapeutic interventions and exhibited a 23.1% higher incidence of thin body condition (p < 0.05) and 10 times more animals with depressed behavior than T1 (p < 0.05). The piglets vaccinated for L. intracellularis (T2 and T3) had rectal temperatures exceeding 39.7 °C post-vaccination, significantly higher than in T1 (p < 0.05). The T1 animals showed five times more positive behavior traits 24 h after vaccination (p < 0.05). Touch response was 29% lower in the T2 and T3 groups, and the lying down behavior was higher in these groups compared to T1. Additionally, 41.7% of the T3 animals exhibited a sitting posture 48 h after vaccination. Higher serum C-reactive protein and haptoglobin levels were observed in T3 (p < 0.05) at 24 and 48 h post-vaccination. Feed intake was higher in T1 compared to T3 between 29 and 35 days of age. It is important to note that this study did not measure immune responses to the pathogens and did not include challenge tests, and therefore, it does not assess which vaccine is superior in pathogen control. Conclusions: The vaccine programs resulted in similar zootechnical performance. However, T1, T2, and T4 showed better effects on piglet welfare and behavior compared to T3.
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