In the search for alternative practices to chemical soil fumigation (CSF), anaerobic soil disinfestation (ASD) has proven to be a promising tool for soil-borne pest management and crop production improvement. The ASD treatment with composted poultry litter (CPL) and molasses (M, a labile carbon source) was identified as an effective approach for a biologically based soil disinfestation system in tomato (Solanum lycopersicum L.) production in Florida. However, environmental and food-safety concerns are associated with animal manure-based amendments, which led to the exploration of composted yard waste (CYW) as a potential substitute for CPL in ASD application. In this study, field trials were conducted in Citra and Immokalee, FL to examine the effects of ASD using CYW, CPL and M compared with a commercially available microbial amendment system on root-knot nematodes, weeds, fruit yield and quality of fresh-market tomato. Treatments included (1) ASD with CPL (11 Mg ha−1) and M (6.9 m3 ha−1) (ASD0.5), (2) ASD with CYW (26.9 Mg ha−1) and M (CYW1 + M), (3) ASD with CYW (13.5 Mg ha−1) and M (CYW0.5 + M), (4) Soil Symphony Amendment (SSA), (5) CYW (26.9 Mg ha−1) alone (CYW1) and (6) a combination of CYW1 + SSA, in comparison with (7) untreated control and (8) CSF (Pic-Clor 60 at 224 kg ha−1). Cumulative soil anaerobiosis was greater in ASD0.5 compared with all the other treatments. The root-knot nematode gall index ratings on the tomato crop were significantly lower in CSF, ASD0.5, CYW1 + M and CYW0.5 + M than untreated control in Citra. Although CYW1 and SSA alone had a moderately suppressive effect on weed coverage and root-knot nematodes, their positive impact on crop performance was limited when used alone. ASD0.5, CYW1 + M and CSF had significantly higher marketable and total fruit yields than untreated control in both locations, while all treatments showed promising results in the Immokalee trial in comparison with untreated control. In general, few differences in major fruit quality attributes were found. Although using CYW in ASD was not as effective as CPL in creating soil anaerobic conditions, the enhanced crop performance in CYW1 + M and CYW0.5 + M suggests the potential of using CYW as an alternative source of organic amendment in combination with M to achieve benefits similar to those obtained with CPL-based ASD.