The administration of the region had an almost purely military character throughout. Von Kaufman died in 1882, and a committee under Fedor Karlovich Giers (or Girs, brother of the Russian Foreign Minister Nikolay Karlovich Giers) toured the Krai and drew up proposals for reform, which were implemented after 1886. In 1888 the new Trans-Caspian railway, begun at Uzun-Ada on the shores of the Caspian Sea in 1877, reached Samarkand. Nevertheless, Turkestan remained an isolated colonial outpost, with an administration that preserved many distinctive features from the previous Islamic regimes, including Qadis' courts and a 'native' administration that devolved much power to local 'Aksakals' (Elders or Headmen). It was quite unlike European Russia. In 1908 Count Konstantin Konstantinovich Pahlen led another reform commission to Turkestan, which produced in 1909–1910 a monumental report documenting administrative corruption and inefficiency. The Jadid educational reform movement which originated among Tatars spread among Muslims of Central Asia under Russian rule.
In 1897 the railway reached Tashkent, and finally in 1906 a direct rail link with European Russia was opened across the steppe from Orenburg to Tashkent. This led to much larger numbers of ethnic Russian settlers flowing into Turkestan than had hitherto been the case, and their settlement was overseen by a specially created Migration Department in Saint Petersburg (Переселенческое Управление). This caused considerable discontent amongst the local population as these settlers took scarce land and water resources away from them. In 1916 discontent boiled over in the Basmachi Revolt, sparked by a decree conscripting the natives into labour battalions (they had previously been exempt from military service). Thousands of settlers were killed, and this was matched by Russian reprisals, particularly against the nomadic population. Order had not really been restored by the time the February Revolution took place in 1917. This would usher in a still bloodier chapter in Turkestan's history, as the Bolsheviks of the Tashkent Soviet (made up entirely of Russian soldiers and railway workers, with no Muslim members) launched an attack on the autonomous Jadid government in Kokand early in 1918, which left 14,000 dead. Resistance to the Bolsheviks by the local population (dismissed as 'Basmachi' or 'Banditry' by Soviet historians) continued well into the beginning of the 1930s.