A sustainable pathway for valorizing the growing volume of lignin-rich organic feedstocks (LRFs) in emerging economies is to convert them into biochar to sequester carbon and improve soil fertility. However, biochar derived from such LRF may not always show favorable outcomes during soil application. Their interaction with the soil–plant–microbial ecosystem is very complex, and comparative investigations with other common types of biochars are lacking. This study investigated the impact of walnut shell biochar (WSB) and wood chip biochar (WCB) on soil biological properties and crop yield during the growth of Solanum lycopersicum L., and compared them with those of plant waste biochar (PWB) derived from agricultural plant residues. Among biochar variants, only PWB (1% w/w) has increased tomato yield compared to unamended soil. It also showed better carbon mineralization that stemmed from its higher degradability, lower carbon content, and higher H/C ratio. In contrast, WSB showed a relatively higher hydrophobicity, carbonization, and aromaticity that reduced its accessibility to soil microorganisms. Despite these characteristics and higher ash content, WSB did not lower soil enzyme and microbial activity, unlike WCB. At the same time, WSB did not improve crop yield. Mixing WSB (3% w/w) with soil has slightly enhanced the soil carbon stabilization. The high carbon recalcitrance of LRF may necessitate longer aging in soil compared with PWB to showcase any measurable (short/long) benefits to crop yield and soil characteristics.