The Yaghnobi language is most commonly written using a modified Latin alphabet, but the Tajik Cyrillic alphabet is also beginning to be used, with the following modifications:

1) Letter й does not have a capital form, as it never appears at the beginning of a word. Words beginning with ya-, yo- and yu-/yū-/yʏ- are written as я-, ё- and ю-; in a similar way are these combinations written in the middle of the word. For example viyóra is written виёра [vɪ̆ˈjoːra].

2) The usage of letters ӣ and ӯ is difficult to determine. It appears that those letters can be used to distinguish two similar sounding words (e.g. иранка and ӣранка, рупак and рӯпак). It could be that the letter ӣ is also used as a stress marker, as in Tajik.

3) In older texts the Yaghnobi alphabet did not use the letters Ъ ъ and Э э. Instead, the Yaghnobi letters ’ and е covered both the Cyrillic е and э for the sound /e/. In later notation those letters were integrated into the alphabet, so the older form етк was changed into этк to represent [ˈeːtkʰ] (and not *[ˈjeːtkʰ]).

4) The sound combinations /ji/ and /je/ are written е and и. The letter и can have the value */ji/ after a vowel (as it has in Tajik), and the letter ӣ after a vowel has the value */jiː/. The letter е has two values - in word-initial position and after a vowel it is pronounced [jeː]; after a consonant it is pronounced [eː]. Note that /je/ is rare in Yaghnobi and is only found in Tajik or Russian loanwords.

5) The Cyrillic letters Ц ц, Щ щ, Ы ы and Ь ь, which are used by Tajik speakers for writing Russian loanwords, are not used by Yaghnobi speakers. The Russian words are written as they are pronounced by the Yaghnobi speakers, not as they are written originally in Russian. For example, [səmʌˈʎot] aeroplane is самолет/самолёт in Russian/Tajik, but in Yaghnobi it is pronounced [samalɪˈjoːtʰ] or [samajlˈoːtʰ] and written as самалиёт, accordingly.

6) The distinction between /v/ and /w/ is not established in the Cyrillic orthography, but is necessary for writing Yaghnobi. Opinion is divided as to the best means for representing the distinction.