The freshly harvested whole garlic bulbs require the inactivation of peroxidase (POD), polyphenol oxidase (PPO), and
Aspergillus niger
. However, the conventional hot water blanching and modern pretreatment like ultrasound (US) and microwave (MW) cannot individually inactivate both the enzymes and
Aspergillus niger
to the desired levels without compromising the quality of the garlic due to either of the higher process temperatures (> 85 °C) or prolonged treatment times. Therefore, a two-stage sequential US followed by MW pretreatment for garlic bulbs was developed for simultaneous inactivation of POD, PPO, and
Aspergillus niger
to the desired levels and overcome the individual pretreatment drawbacks. The separate experiments were conducted for US and MW pretreatment using central composite design, and optimization was carried out using response surface methodology. When temperature constraint was considered during optimization, the US was able to reduce POD, PPO, and
Aspergillus niger
by 80.87%, 93.80%, and 2.60 logs, respectively, whereas MW reduced POD, PPO, and
Aspergillus niger
by 77.84%, 77.04%, and 1.90 logs, respectively. The US treatment (58.43 WL
−1
ultrasound power density for 40 min with an initial bath temperature of 60 °C) followed by MW treatment (3 Wg
−1
MW power density for 120 s) resulted in 90.37% POD and 92.38% PPO inactivation with 2.62 log reduction in
Aspergillus niger
. The maximum temperature reached in US + MW process was 83 °C which ensured no severe thermal damage to the garlic bulbs. The scanning electron microscopic images indicated that ultrasonication induced the porous structure in garlic and helped microwaves increase the product temperature rapidly and achieve the higher inactivation of enzymes and
Aspergillus niger
. Thus, the US was found to be enhancing the efficacy of the MW heating process.