A service quality report covering April to June showed the operator met 15 out of 38 targets, but fell short in areas including toilets, train cleanliness and litter at stations.
The franchise is fined by Transport Scotland when it breaches performance measures.
More than £1,061,000 of fines were issued for the three-month period.
This followed more than £1,180,000 of penalties between January and March.
Scottish Labour’s transport spokesman Colin Smyth said: “Passengers across Scotland deserve better than this failing ScotRail franchise. The least they can expect for a four-figure season ticket is for trains to be clean, but as these official figures show that is routinely not the case.
“These fines are not worth the paper they are written on, with privately-run ScotRail funded by the taxpayer through subsidies in the first place.”
ScotRail said the money from penalties is reinvested into Scotland’s railways. Pointing to a fall in fines from the first to the second quarter of this year, ScotRail’s David Lister said: “We know there is a lot of work still to be done, but these figures confirm the progress ScotRail is making.
The investment we are making – in new and refurbished trains, in station facilities and in our people – is part of our plan to build the best railway Scotland has ever had.”