<p>The commercial plantation of agar trees has been increasing in the Brahmaputra floodplain under the greater Mymensingh region of Bangladesh. Agar plantation in the plainland allows enough space for cultivating different crops in between the two rows of agar trees. The present field study transformed a commercial agar (<i>Aquilaria malaccensis</i> Roxb.) plantation into agroforestry systems, where the performance of winter vegetables (radish, spinach, broccoli, and tomato) and the annual crop papaya were evaluated at different distances from the tree row. Afterward, it was compared with their respective non-agroforestry sole crops planted in open-field (control) conditions. The findings of the investigation revealed that the yield reduction for radish, spinach, broccoli, and tomato was 40%, 58%, 37%, and 40%, respectively, in agroforestry systems compared to the control. The yields of the seasonal crops were boosted with increasing planting distances from tree rows. These findings also indicated that the light intensity, which is indispensable for crop production, was highly interfered with in the agroforestry system by the straight canopy structure of agar trees. Though having some adverse impacts on yield performances of seasonal crops, the net return, benefit–cost ratio (BCR), and land equivalent ratio (LER) were greatly higher in agar-based agroforestry systems compared to non-agroforestry systems. Compared to non-agroforestry control plots, the total nitrogen, phosphorus, and potassium content in agroforestry systems was 41%, 27%, and 150% higher, respectively. Thus, it can be concluded that the Aquilaria plantation can be transformed into an agroforestry system to ensure higher income, optimum land use, and soil fertility status, and sustain food security.</p>