This study investigated the phytotoxicity of agro-industrial wastes (almond, walnut, pistachio and peanut shells, asparagus spears, and brewer’s spent grain) and their biochar through germination bioassays in several horticultural species: green pea, lettuce, radish, and arugula. Biowaste was pyrolyzed under controlled conditions to produce biochar, and both biowaste and biochar were characterized. Germination bioassay was conducted using seeds exposed to different dilutions of aqueous extract of biowaste and their biochar (0, 50, and 100%). Germination percentage, seed vigor, germination index, and root and aerial lengths were evaluated. The results showed that the phytotoxicity of the biowaste was significantly different to that of its biochar. The biochar obtained demonstrated changing effects on germination and seedling growth. In particular, biochar extracts from spent brewers grains, walnut shells, and pistachio shells showed 5–14% increases in seed vigor and root and aerial length. Furthermore, the response of different species to both agro-industrial waste and biochar revealed species-specific sensitivity. Seeds of lettuce and arugula species were more sensitive to aqueous extracts than radish and green peas. This knowledge not only elucidates the behavior of agro-industrial waste-based biochar in the early stage of plant development but also provides valuable insights regarding phytotoxicity, seed sensitivity, and the variables involved in germination.