Kammala jumla mai zuwa: Johnston ya kasance mai farin ciki game da fashewar yakin Mexican-American. Ya yi aiki a kan ma'aikatan Laftanar Janar Winfield Scott a cikin
Siege na Veracruz, wanda Scott ya zaba ya zama jami'in da ke dauke da bukatar mika wuya a gaba ga gwamnan lardin. Ya kasance a cikin jagorancin motsi na cikin gida a karkashin Brig. Janar David E. Twiggs kuma ya ji rauni sosai ta hanyar yin bincike kafin yakin Cerro Gordo. An nada shi a matsayin Laftanar Kanar don ayyukansa a Cerro Gordo. Bayan ya dawo cikin asibitin filin, sai ya koma soja a Puebla. A lokacin ci gaba zuwa Mexico City, shi ne mataimakin kwamandan "Jami'ar Voltigeurs ta Amurka", wani rukuni da ke kunshe da 'yan bindiga ko' yan bindiga. Ya bambanta kansa a Contreras da Churubusco, an sake ji masa rauni a Chapultepec, kuma ya sami ci gaba guda biyu don abubuwan biyu na ƙarshe, ya ƙare yakin a matsayin mai kula da masu sa kai. (Bayan ƙarshen tashin hankali, ya koma matsayinsa na zaman lafiya na kyaftin a cikin injiniyoyi na topographical.) Winfield Scott ya yi tsokaci cikin raha cewa "Johnston babban soja ne, amma yana da rashin sa'a na samun kansa harbi a kusan kowane rikici". Babbar wahalar Johnston a lokacin yakin ita ce mutuwar dan uwansa, Preston Johnston. Lokacin da Robert E. Lee ya sanar da Johnston cewa an kashe Preston ta hanyar bindigar bindigar Mexico a Contreras, jami'an biyu sun yi kuka, kuma Johnston ya yi baƙin ciki har tsawon rayuwarsa.