Three biochars were prepared by intermediate pyrolysis from poultry litter at different temperatures (400, 500, and 600 °C with decreasing residence times) and compared with biochars from corn stalk prepared under the same pyrolysis conditions. The phytotoxicity of these biochars was estimated by means of seed germination tests on cress (Lepidium sativum L.) conducted in water suspensions (at 2, 5, and 40 g/L) and on biochars wetted according to their water-holding capacity. Whereas the seeds germinated after 72 h in water suspensions with corn stalk biochar were similar to the control (water only), significant inhibition was observed with poultry litter biochars. In comparison to corn stalk, poultry litter generated biochars with higher contents of ash, ammonium, nitrogen, and volatile fatty acids (VFAs) and a similar concentration of polycyclic aromatic hydrocarbons (PAHs). Results from analytical pyrolysis (Py-GC-MS) indicated that nitrogen-containing organic compounds (NCCs) and aliphatic components were distinctive constituents of the thermally labile fraction of poultry litter biochar. The inhibition of germination due to poultry litter biochar produced at 400 °C (PL400) was suppressed after solvent extraction or treatment with active sludge. A novel method based on solid-phase microextraction (SPME) enabled the identification of mobile organic compounds in PL400 capable of being released in air and water, including VFAs and NCCs. The higher phytotoxicity of poultry litter than corn biochars was tentatively attributed to hydrophilic biodegradable substances derived from lipids or proteins removable by water leaching or microbial treatments.