Accommodation in Kosovo can be expensive, meaning it is probably the same as hotels in surrounding countries starts at €25 and goes over €100 and primarily is designed for people working for the development agencies. Your best bet on finding a place to stay is outside of Prishtina if you're with the car and to have a contact there ahead of time even if its just somebody you met over the internet and stay with them. Or possibly contact some of the smaller development organisations, such as Balkan Sunflowers and online listing of Kosovo hotels, and ask if they can help you with accommodation staying in a rural community or in the city for a higher price.

Skopje in Macedonia has some very cheap accommodation, so doing day trips to Kosovo from there is very much a possibility. But Prishtina now has many places; thus, there is no need to go and come back from Skopje just for a cheap hotel for a night.