Once Shoin was executed in the Ansei no Taigoku (suppression of extremists by the Shogunate) in 1859, Shinagawa joined Shinsaku TAKASUGI and gave himself to the Sonno Joi (reverence for the Emperor and the expulsion of foreigners) movement, involving himself in such actions as fire attacks on the British Legation.
安政7年（1859年）に安政の大獄で松陰が刑死すると、高杉晋作らと行動を共にして尊王攘夷運動に奔走し、イギリス公使館焼き討ちなどを実行している。