Kutsawar da dan mamaye na kasar Spain din Don Nuño Beltrán de Guzmán ya yi zuwa kasashen yammacin kasar, don kara karfin mulkinsa da ikonsa a wadannan yankuna, ya haifar da kafa sabon lardin da ake kira Masarautar New Galicia.
Wasungiyoyin 'yan asalin yankin daban-daban ne ke zaune a yankin, waɗanda ke ci gaba da lalata ƙauyukan da Mutanen Espanya suka kafa a ciki. Laftanar Nuño de Guzmán, Kyaftin Juan B. de Oñate ya karɓi umarni don kwantar da hankulan waɗancan lardunan tare da gano Villa de Guadalajara a wurin da ake kira Nochistlán, gaskiyar da ya gama a ranar 5 ga Janairu, 1532. Ganin yawan hare-haren 'yan asalin ƙasar da ake yawan kaiwa a birnin. dole ne ya koma shekara guda zuwa Tonalá sannan daga baya ya koma Tlacotlán. Canja wuri na uku da aka yi don daidaita garin a cikin kwarin Atemajac, inda aka kafa garin sosai a ranar 14 ga Fabrairu, 1542 tare da kasancewar Cristóbal de Oñate a matsayin gwamnan New Galicia da Don Antonio de Mendoza, sannan mataimakin magajin New Spain, wanda ya nada Miguel de Ibarra magajin gari kuma Laftana gwamna.
Birnin ya haɓaka cikin sauri kuma ya fara gasa tare da na Compostela (a yau Tepic), wanda a lokacin shine wurin zama na ikon addini da na farar hula, don haka mazaunan Guadalajara suka matsa lamba ga hukumomin Audiencia, cewa sarki Felipe II ya yanke shawarar bayar da Takaddun kwanan wata 10 ga Mayu, 1560 don ya tashi daga Compostela zuwa Guadalajara, Cathedral, Royal Court da kuma baitul mali.
Tsarin birni an tsara shi bisa ga na sauran biranen mulkin mallaka, don haka aka tsara fasalin sa ta hanyar tebur daga abin da yake filin San Fernando. Daga baya Fray Antonio de Segovia ya kafa unguwannin Mexicaltzingo da Analco, da kuma unguwar Mezquitán, ɗayan tsofaffi. Hakanan an gina gidajen zauren gari, a gaban haikalin San Agustín na yanzu da cocin farko na Ikklesiya inda Fadar Adalci take.
A yau, babban birni, mai yawan gaske a cikin gine-ginen mulkin mallaka, yana nuna adadi mai yawa na misalan gine-ginen da suka dace, kamar su Cathedral, wani wurin gani-gani, wanda aka gina tsakanin 1561 da 1618 ta mai ginin Martín Casillas. An tsara salon sa a matsayin mai ƙarancin baroque. Tsarinsa mai ƙarfi ya tashi a gaban Plaza de Guadalajara na yau, tare da hasumiyoyi masu ban sha'awa waɗanda, kodayake ba sa cikin asalin salon ginin, amma a halin yanzu an san su a matsayin alama ta babban birnin Guadalajara. An lalata hasumiyai na farko a ƙarni na 19 ta hanyar girgizar ƙasa, wanda shine dalilin da ya sa aka ƙara waɗanda yake da su a yau. Cikin gidan haikalin yana cikin salon Semi-Gothic, gami da mafakarsa waɗanda aka yi da yadin da aka saka.
Sauran yankuna na addini daga karni na 16 sune san Francisco convent, wanda aka kafa a 1542 kusa da kogi, a cikin yankin Analco, kuma kusan an lalata shi gaba daya a cikin gyarawa. Haikalinta, wanda aka sake gyara shi a ƙarshen karni na 17, tare da fasalin Baroque na layukan Sulemanu masu kyau, ana kiyaye shi. Gidan zuhudu na San Agustín, an kafa shi ne a 1573 ta Dokar Sarauta ta Felipe II kuma a halin yanzu tana kiyaye haikalinta tare da fuskoki na manyan layukan Herrerian da cikin ta tare da ribbbed vaults.
Santa María de Gracia, wani daga cikin ginshiƙan ginin, mazaunan Dominican ne suka zauna daga Puebla, wanda aka gina a 1590 a gaban Plaza de San Agustín kuma Hernán Gómez de la Peña ne ya biya kuɗin. Ginin ya kasance ya mamaye bangarori shida, kodayake a yau kawai haikalinsa yana ci gaba, tare da facin neoclassical daga rabi na biyu na karni na 18.
