Allium crops including shallot have been reported to have a high dependency on symbiosis with arbuscular mycorrhizal fungi (AMF), and have a high requirement for fertilizers. This study aimed to examine the effects of additively intercropping shallot with peanut and application of different combinations of organic-silicate-mycorrhiza-bio-fertilizer on growth and yield of several varieties of shallots. The field experiment for this study was designed according to Split Split-Plot design, with three blocks and three treatment factors, namely additive intercropping as the main plots (T0 = without; T1 = with shallot-peanut intercropping), shallot varieties as the subplots (V1 = Bima Brebes; V2 = Ketamonca; V3 = Super Philip), and fertilizer combinations as the sub-subplots (P1 = NPKS fertilizer only; P2 = NPKS+organic+silicate; P3 = NPKS+organic+silicate+mycorrhiza bio-fertilizer). Results indicated that among the treatment factors, fertilizer combination showed the most significant effects on growth and yield of shallot, and both fertilizer combinations containing silicate and organic fertilizer (P2 and P3) significantly increased yield of shallot, especially the P3 fertilizer combination, which contained mycorrhiza bio-fertilizer. Although intercropping with peanut showed no significant effects on all observation variables, there was a significant three-way interaction effect on shallot yield, which indicated different responses between varieties to intercropping and fertilizer combinations, in which yield of Ketamonca (V2) was not affected by intercropping but yield of Bima Brebes (V1) was reduced by intercropping, whereas yield of Super Philip (V3) was increased by intercropping it with peanut, especially under fertilizer combination containing mycorrhiza bio-fertilizer (P3).