A farkon karni na 16, bayan da Daular Usmaniyya ta mamaye kasar Masar a shekara ta 1517, Sultan Selim na daya ya nada Yunus Pasha a matsayin gwamnan Masar, amma ba da dadewa ba aka maye gurbinsa da Hayır Bey saboda matsalar cin hanci da rashawa.^[97] Wannan lokacin ya nuna gwagwarmayar iko tsakanin wakilan Ottoman daMamluks , waɗanda suka ci gaba da tasiri mai mahimmanci.An shigar da Mamluks cikin tsarin gudanarwa, suna rike da manyan mukamai a sanjak 12 na Masar.A karkashin Sultan Suleiman Mai Girma, an kafa Greater Divan da Lesser Divan don taimakawa pasha, tare da wakilci daga sojoji da hukumomin addini.Selim ya kafa runduna shida don kare Masar, wanda Suleiman ya kara na bakwai.^[98]Gwamnatin Ottoman tana yawan canza gwamnan Masar, sau da yawa a kowace shekara.Wani gwamna Hain Ahmed Pasha ya yi yunkurin kafa 'yancin kai amma aka ci tura aka kashe shi.^{[98 [98] <]} > A cikin 1527, an gudanar da binciken ƙasa a ƙasar Masar, inda aka rarraba ƙasa zuwa nau'i huɗu: yankin sarkin musulmi, fifs, filin kula da sojoji, da filayen tushe na addini.An aiwatar da wannan binciken a shekara ta 1605. ^[98.]Karni na 17 a Masar ya kasance da tashe-tashen hankula na soji da kuma tashe-tashen hankula, sau da yawa saboda yunƙurin da ake yi na hana kwace da sojoji ke yi.A cikin 1609, wani gagarumin rikici ya kai ga nasarar Kara Mehmed Pasha shiga Alkahira, sannan gyare-gyaren kudi ya biyo baya.^{[98 <>]} A wannan lokacin, Mamluk beys na gida ya sami rinjaye a cikin gwamnatin Masar, yawanci yana rike da mukaman soja kuma yana kalubalantar gwamnonin da Ottoman ya nada.^[99] <> Sojojin Masar, masu ƙaƙƙarfan alaƙar gida, suna yawan yin tasiri ga nadin hakimai kuma suna da iko sosai akan gudanarwa.^[100]Ƙarni kuma ya ga bunƙasa ƙungiyoyi biyu masu tasiri a Masar: Faqari, waɗanda ke da alaƙa da sojan dokin Ottoman, da kuma Qasimi, waɗanda ke da alaƙa da sojojin Masar na asali.Waɗannan ƙungiyoyin, waɗanda ke da alamar launukansu da alamominsu, sun yi tasiri sosai a harkokin mulki da siyasar Ottoman Masar.^[101]