Bacterial heart rot (BHR) disease in pineapple variety MD2 is caused by Dickeya zeae syn. Erwinia chrysanthemi. The present study aims to screen the effectiveness of four systemic chemical pesticides in different dosages for controlling the BHR pathogen in vitro and to evaluate the effectiveness of delivery techniques of the selected chemical pesticides based on in vitro results to control the disease under rain shelter conditions. The pathogen was isolated from symptomatic pineapple leaves with the appearance of water-soaked and rotten basal tissues and confirmed via pathogenicity test. A poisoned food technique was used for in vitro assessment. The pathogen was tested with different pesticide concentrations of 250, 500, 750, 1000 and 1500 mg L−1. Two fungicides were selected based on in vitro study for further investigation under the rain shelter condition. This in vivo study was performed with arrangement of complete randomize design with five treatments and 10 replicates of pineapple plants per treatment. The treatments were difenoconazole with pathogen, mancozeb with pathogen, benomyl with pathogen (standard industry), positive control (pathogen only) and negative control (without pathogen). Data of disease incidence (DI) and disease severity index (DSI) were collected for six-weeks after the early symptoms of BHR were detected. Finding of in vitro study showed that mancozeb and difenoconazole were able to control the pathogen at the lowest concentration of 250 mg L−1 from the recommended rate. These two fungicides were consistently giving the similar results for the rain shelter study. The treatments with difenoconazole recorded the lowest value of DI and DSI with 4.60% and 0.00%, respectively. Then followed by mancozeb with DI of 5.62% and 63.71%. In contrast, besides positive control, the treatment of benomyl displayed the high values of DI (8.38%) and DSI (89.81%). Based on these findings, difenoconazole with combination method is the most effective control method for controlling BHR in pineapple. However, this research is highly recommended to be further investigated under the field conditions.