A combination of matrix-assisted laser desorption ionization (MALDI) imaging and infrared (IR) laser ablation sampling with offline electrospray ionization mass spectrometry (ESI-MS) was used to determine the distribution of the fungicide imazalil in apples. MALDI images were used to determine the penetration depth of imazalil up to 7 days after its application. IR laser ablation sampling and ESI-MS were used to quantify the rate of penetration of the fungicide, which was determined to be approximately 1 mm per day. Imazalil concentration decreased in the apple skin over the course of the experiment, and after 7 days the fungicide was detected at 0.015 ppm 6 mm inside the apple. Approximately 60% of the pesticide remained in the skin after 7 days. This work demonstrates the utility of MALDI imaging for spatial localization of fungicide in fruit in combination with IR laser ablation and ESI-MS for quantitative analysis.