Update
With biblatex v3.18 and above you can use \localrefcontext and \GenRefcontextData to switch to a different reference context (e.g. sorting).
Use
\AtBeginRefsection{\GenRefcontextData{sorting=ynt}}
to make sure that each refcontext our document uses also generates an analogous refcontext with ynt sorting.
Then
\AtEveryCite{\localrefcontext[sorting=ynt]}
switches our citations to the ynt sorting refcontext. \localrefcontext only acts locally and need not be "closed" or reset because it happens inside a group.
\documentclass{article}
\usepackage[backend=biber,
style=authoryear-comp,
% sortcites=true, % not needed here because it is implied by style=authoryear-comp,
]{biblatex}
\AtBeginRefsection{\GenRefcontextData{sorting=ynt}}
\AtEveryCite{\localrefcontext[sorting=ynt]}
\begin{filecontents}{\jobname.bib}
@book{key2000,
author = {Author, A.},
year = {2000},
title = {Alphabetical fist & Year last},
publisher = {Publisher},
}
@book{key1900,
author = {Boathor, B.},
year = {1900},
title = {Alphabetical last & Year first},
publisher = {Publisher},
}
\end{filecontents}
\addbibresource{\jobname.bib}
\begin{document}
Lorem \autocite{key2000, key1900}
ipsum \autocite{key1900, key2000}
\printbibliography
\end{document}

See also Sort citations by year (ynt) and references by name (nyt) in custom biblatex style.
Solution for older versions of biblatex
Give the desired citation sort order at loading time. Then give the desired order for the bibliography in the new refcontext (\begin{refcontext}[sorting=<sorting>]...\end{refcontext}) for \printbibliography.
\documentclass{article}
\usepackage[backend=biber,
style=authoryear-comp, sorting=ynt,
% sortcites=true, % not needed here because it is implied by style=authoryear-comp,
]{biblatex}
\begin{filecontents}{\jobname.bib}
@book{key2000,
author = {Author, A.},
year = {2000},
title = {Alphabetical fist & Year last},
publisher = {Publisher},
}
@book{key1900,
author = {Boathor, B.},
year = {1900},
title = {Alphabetical last & Year first},
publisher = {Publisher},
}
\end{filecontents}
\addbibresource{\jobname.bib}
\begin{document}
Lorem \autocite{key2000, key1900}
ipsum \autocite{key1900, key2000}
\begin{refcontext}[sorting=nyt]
\printbibliography
\end{refcontext}
\end{document}

I used
\begin{refcontext}[sorting=nyt]
\printbibliography
\end{refcontext}
instead of the slightly shorter
\newrefcontext[sorting=nyt]
to be on the safe side if there are citations after the bibliography.
Hints and Caveats
Some more explanation since this comes up more often.
biblatex does not allow the sorting option for \printbibliography any more. It was removed because it could lead to weird sorting results.
Instead, now you use 'refcontexts' to control sorting. A refcontext controls sorting, labelprefix and sortingnamekeytemplate and a few other things (possible more in the future).
An entry can appear in different refcontexts and any extra label data (extradate, extraalpha) will be recalculated based on the specific details (e.g. sorting) for each refcontext.
This can lead to slightly counter-intuitive results in very contrived examples because the sort order may be determined by data that is invisible in the citation itself and those data leads to different sorting results in different schemes.
Here is an admittedly very artificial example that shows this behaviour with your set-up. It can be much easier to achieve such an effect with other pairings of sort schemes. The trick here was that nyt considers the volume for sorting while ynt does not.
\documentclass{article}
\usepackage[backend=biber, style=authoryear, sorting=ynt, sortcites]{biblatex}
\usepackage{hyperref}
\begin{filecontents}{\jobname.bib}
@book{one,
author = {Elk, Anne},
title = {Title},
volume = {1},
note = {sorts first in ynt},
}
@book{two,
author = {Elk, Anne},
title = {Title},
note = {sorts first in nyt},
}
\end{filecontents}
\addbibresource{\jobname.bib}
\begin{document}
\autocite{one,two} \autocite{two,one}
\begin{refcontext}[sorting=nyt]
\printbibliography[title={\refname{} (sorting \texttt{nyt})}]
\end{refcontext}
\end{document}
![(Elk n.d.[b]; Elk n.d.[a]) (Elk n.d.[b]; Elk n.d.[a])](../../images/291db305a87fa59e89083b83c580feb7.webp)
sortingoption has been moved from\printbibliographyto so called 'refcontexts'. See Biblatex order of entries in a multi-citation. And the default is that all citations obey the refcontext they were last printed in the bibliography. So simply using a globalsortingthat contradicts the\printbibliography'srefcontext'ssortingdoes not work – moewe Mar 29 '17 at 14:24sortcites=falseand manually sorting references within citation... but I wanted to be lazy and make (Bib)LaTeX do it for me! | Just to be sure to understand your previous comment: the sorting scheme chosen, is the one of therefcontextselected whenprintbibliographyis called and not at the time of the\citecommand, right? (I tried to add\newrefcontext[sorting=ynt]right after\begin{document}+ what I added in my P.S, but it indeed doesn't work.) – ebosi Mar 29 '17 at 14:32\printbibliography. There are ways to manually assign the refcontext (i.e. override the 'use the refcontext of the last bibliography' rule). But you need to be careful about potentially different extrayears. – moewe Mar 29 '17 at 14:33