Propane flaming in combination with cultivation could be a potential alternative tool for weed control in organic soybean production. Field experiments were conducted at the Haskell Agricultural Laboratory of the University of Nebraska-Lincoln (UNL), Concord, NE in 2010, 2011 and 2012 to determine the level of weed control and the response of soybean grain yield and its components to flaming and cultivation within two fertility regimes (FRs) (with and without manure) utilizing flaming equipment developed at the UNL. The treatments included: weed-free control, weedy season-long and different combinations of banded flaming (intra-row), broadcast flaming and mechanical cultivation (inter-row). The treatments were applied at VC (unfolded cotyledon) and V4–V5 (4-leaf–5-leaf) growth stages. Propane doses were 20 and 45 kg ha−1 for the banded and broadcast flaming treatments, respectively. The data were collected for visual ratings of crop injury and weed control at 7 and 28 days after treatment (DAT) at V4–V5 growth stages, weed dry matter at 60 DAT, crop yield and yield components. The annual application of 101 t ha−1 manure did not alter weed community or influence the effectiveness of weed management treatment; however, it decreased soybean yield by 0.25 t ha−1 through an increased weed biomass of 0.16 t ha−1. The weed-free control plots yielded 4.15 t ha−1. The combination of mechanical cultivation and banded flaming applied twice (at VC and V4–V5) was the best treatment resulting in 80–82% weed control and 6–9% crop injury at 28 DAT and 3.41–3.67 t ha−1 yield. Cultivation conducted twice provided only 19% weed control at 28 DAT and 1.75 t ha−1 yield. Soybean plants recovered well after all flaming treatments, with the exception of broadcast flaming conducted twice (28% crop injury at 28 DAT). Combining flaming with cultivation has a potential to effectively control weeds in organic soybean production across a range of FRs.