Kukumana kosalekeza kwa wogonjetsa waku Spain a Don Nuño Beltrán de Guzmán kulowera kumadzulo kwa dzikolo, kuti awonjezere ulamuliro wake ndi mphamvu zake m'malo amenewo, zidapangitsa kuti pakhale chigawo chatsopano chotchedwa Kingdom of New Galicia.
M'derali munkakhala anthu azikhalidwe zosiyanasiyana, omwe amapitiliza kuwononga midzi yomwe a Spain adakhazikitsako. Lieutenant wa a Nuño de Guzmán, a Captain Juan B. de Oñate adalamulidwa kuti akhazikitse bata zigawozi ndikupeza Villa de Guadalajara pamalo otchedwa Nochistlán, zomwe adazimaliza pa Januware 5, 1532. Poona kuzunzika kwanthawi zambiri kwa mzindawu adasamukira chaka chimodzi kupita ku Tonalá ndipo kenako ku Tlacotlán. Kusamutsidwa kwachitatu kunapangidwa kuti akakhazikitse tawuni ya Atemajac Valley, pomwe mzindawu udakhazikitsidwa motsimikizika pa February 14, 1542 pomwe Cristóbal de Oñate anali kazembe wa New Galicia ndi Don Antonio de Mendoza, ndiye wolowa m'malo mwa New Spain, yemwe adasankha meya wa Miguel de Ibarra komanso kazembe wa lieutenant.
Mzindawu udakula mwachangu ndipo udayamba kupikisana ndi wa Compostela (masiku ano Tepic), yemwe panthawiyo anali likulu la zipembedzo ndi maboma, kotero kuti nzika zaku Guadalajara zidakakamiza olamulira a Audiencia, kuti mfumu Felipe II adaganiza zopanga Cédula ya Meyi 10, 1560 kuti achoke ku Compostela kupita ku Guadalajara, Cathedral, Royal Court ndi akuluakulu azachuma.
Kapangidwe kamatauni kamakonzedwa molingana ndi mizinda ina yamakoloni, motero kamangidwe kake kanapangidwa ngati chessboard kuchokera komwe kunali malo a San Fernando. Pambuyo pake madera a Mexicaltzingo ndi Analco adakhazikitsidwa ndi Fray Antonio de Segovia, ndi madera a Mezquitán, amodzi mwa akale kwambiri. Nyumba zamatawuni zamzindawu zidamangidwanso, kutsogolo kwa kachisi wamakono wa San Agustín ndi tchalitchi choyamba cha parishi komwe kuli Nyumba Yachilungamo.
Masiku ano, mzinda wokongola kwambiri, wokhala ndi nyumba zachikoloni, ukuwonetsa zitsanzo zingapo zomanga, monga Cathedral yake, malo oyenera kuwona, omangidwa pakati pa 1561 ndi 1618 ndi katswiri wa zomangamanga Martín Casillas. Machitidwe ake amadziwika kuti ndi obiriwira. Kapangidwe kake kolimba kamayang'ana kutsogolo kwa Plaza de Guadalajara lero, ndi nsanja zake zokongola zomwe, ngakhale sizili zoyambirira za nyumbayo, pano zimadziwika ngati chizindikiro cha likulu la Guadalajara. Nsanja zakale zidawonongedwa m'zaka za zana la khumi ndi chisanu ndi chinayi ndi chivomerezi, motero zomwe zilipo lero zawonjezedwa. Mkati mwake mwa kachisiyu muli kalembedwe ka Gothic, kuphatikiza zipinda zake zopangidwa ndi zingwe.
Madera ena azipembedzo ochokera m'zaka za zana la 16 ndi nyumba yachifumu ya San Francisco, yomwe idakhazikitsidwa mu 1542 pafupi ndi mtsinje, mdera la Analco, ndipo idawonongedwa kwathunthu mu Reformation. Kachisi wake, wokonzedwanso kumapeto kwa zaka za zana la 17, ndimipanda yake ya Baroque yokhala ndi mizere yocheperako ya Solomon, yasungidwa. Msonkhano wa San Agustín, womwe unakhazikitsidwa mu 1573 ndi Royal Ordinance wa Felipe II ndipo pano umasunga kachisi wake wokhala ndi mizere yolimba ya Herrerian komanso mkatimo mwake wokhala ndi zipinda zovundikira.
Santa María de Gracia, amodzi mwa maziko amatchalitchi, anali ndi agulupa achi Dominican ochokera ku Puebla, omangidwa mu 1590 kutsogolo kwa Plaza de San Agustín ndipo amalipira ndi Hernán Gómez de la Peña. Ntchito yomangayi idakhala ndi mipanda isanu ndi umodzi, ngakhale lero kuli kachisi wake yekha, wokhala ndi neoclassical facade kuyambira theka lachiwiri la zaka za zana la 18.
