Beneficial effects of bio-inoculants on growth and yield of plants grown in sunlight have been reported world over but information on their effect under shade is meagre. Therefore, to assess the effect of shade on bio-inoculants, viz. rhizobial (RB) and phosphate-solubilizing bacteria (PSB), and arbuscular mycorrhizal fungi (AMF), which are associated with intercrops in agroforestry systems, a study was carried out on important rainy (Glycine max, Phaseolus mungo, and Vigna radiata) and winter season pulses (Cicer arietinum, Lens culinaris, and Pisum sativum) under 25% (shade) and 100% (no shade) full sun light. The results showed that plant height was higher under the shade in G. max, P. mungo, L. culinaris, and P. sativum, and lower in V. radiata and C. arietinum. Dry weight and yield plant−1 were lower under the shade than the corresponding values in the open for all pulses. In general, bio-inoculants increased plant height, dry weight, and yield plant−1 in all pulses, barring a few exceptions. The efficiencies of bio-inoculants in terms of percent increase of yield over respective control were more or less comparable under shade and no shade for most pulses. The shade reduced rhizobial nodulation and AMF colonization in all crops with a few exceptions. Application of bio-inoculants increased the nodulation and the colonization in most of the treatments. Maximum yield plant−1 was recorded in dual and/or triple inoculations under both shade and no shade suggesting that the bio-inoculants used in our study worked synergistically with each other. Thus, the studied bio-inoculants were effective in the open as well as in the shade and can be utilized to overcome the adverse effect of shade to some extent in agroforestry systems.