The study aimed to determine the effect of indogenous non-symbiotic fungi isolates on growth and yield of shallots (Allium ascalonicum L.) on planting media contaminated Pb heavy metal. It was conducted at 1) Green House of Faculty of Agriculture, Universitas Muhammadiyah Purwokerto, 2) Karangsari Village, Kembaran sub-district, Banyumas Regency, 3) Basic Agrotechnology Laboratory of the Faculty of Agriculture, Universitas Muhammadiyah Purwokerto, 4) Microbiology Laboratory of Teacher Training and Education Faculty (FKIP ) Universitas Muhammadiyah Purwokerto, and 5) the Laboratory of Land Resources of Faculty of Agriculture, Universitas Jendral Soedirman from December 2018 to July 2019. The study implemented one-factor Completely Randomized Design (CRD) method. The treatments provided were 3 levels; F0 (non-fungi), F1 (Penicillium cf citrinum) and F2 (Trichoderma cf harzianum). The data obtained were analyzed through F test and if the result presented a significant effect then it was continued to DMRT test with level of 5%. The results revealed that the isolate treatment gave no significant effect to the observation variables of total leaf length, number of leaves, fresh weight of plants, fresh weight of leaves, and fresh weight of tubers. However, Penicillium cf citrinum isolate significantly affected the total root length. Levels test on Pb of shallot tubers F0 (3.49 ppm), F1 (2.91 ppm) and F2 (3.98 ppm). The planting media after harvest indicated that both fungi were still available.