In medieval Europe the church was a major landowner, and for example monasteries would often own much of the surrounding land (at least this was the case in Germany but I would assume elsewhere too).
I am wondering if there were any general differences between how the peasants were treated if their lord was a noble compared to if they belonged to the church? Taxes, laws, administration etc.
tl;dr - Very occasionally we can point to a concrete difference, but in general it sucked to be a peasant under an ecclesiastical or a secular lord--despite the Church purporting to stand for the safety of the peasants and denouncing the violence of lay lords.
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Although the line between "consecrated cleric" and "previous lord's son" seems obvious, the realities of medieval power and nobility blurred the line almost before it was drawn. Abbots and bishops of prestigious, politically important houses and dioceses--the ones who would be ecclesiastical lords--were drawn from the upper echelons of the nobility themselves, raised and steeped in the same lordly culture. These are not your St. Francis or even your Otto von Freising--they're the sons (or daughters, often ruling through a male proxy) of the same lords as their lay counterparts, ambitious and educated and using the Church as a vehicle for power. Ecclesiastical lords moved in the same social and cultural circles as their lay counterparts, exchanging manuscripts of profane and sacred literature alike.
The Church did try to ban its lords from engaging in certain practices (for example, capital punishment), so bishop-lords created a "lay advocacy" position--with the Church and the bishop-lord having free reign to get rid of any lay advocate they disliked, of course.
And in some cases, secular lords could usurp the privileges usually reserved for ecclesiastical figures: Roger of Sicily got himself elected as a papal legate in the 11th century, for example, giving him the right to deal directly with the churches and bishop-lords of Sicily without needing approval from the pope for each ruling.
Ecclesiastical lords typically had all the powers of lay lords, including legal jurisdiction. For example, there are a few places in twelfth-century France where a women's monastery held huge...tracts of land, and chronicles note that the abbess presided over suits brought by disgruntled peasants. In the Holy Roman Empire, bishop-lords and lay lords ruled their territories the same way, with the cathedral chapter (group of clerics) serving in the Church districts the same advisory-type function as the Landstände/Estates of under-lords in lay lands.
Sometimes, though, a prince or king found it advantageous to endow ecclesiastical lords over lay lords. Roger maneuvered to get the papal legateship, for example, as part of a strategy to maintain control over his newly-conquered island. He partitioned Sicily among more ecclesiastical lords instead of lay lords, then used his legate status to impose much stricter conditions on the bishops and abbots than he would have been able to place on lay lords in fortified castles. In return, of course, the Norman rulers richly patronized the cathedrals and monasteries of Sicily.
Life for peasants? Well, it can be a challenge to tease out the behavior of ecclesiastical lords for most of the Middle Ages, since the bulk of protests against violent lordship come from Church synods (councils). They were, shall we say, much more enthusiastic about condemning wayward secular lords than their own brethren when it came to violence. (Much sharper on the condemnations for financial abuse and sexual transgressions, naturally--because ecclesiastical lords makin' bank for themselves hurt the Church and its image, and makin' offspring for themselves opening the door to future nepotism).
There are, however, a few high medieval cases of ecclesiastical lords being sharply sanctioned for violence. In 1049, the Synod of Rheims deposed and excommunicated Bishop Hugh of Langres (today, in northeastern France) for vicious armed actions, homicides against his peasants, working with nearby lords and vassals to be even more violent, and tyranny in general (tyrannus is the big buzz word in 11th/12th century discussions of bad lords).
By the time you get to the brink of the Reformation in the late 15th/early 16th century, peasants are equally unhappy with ecclesiastical and secular lords. They complain about the same types of things, from violent raids to restrictions on water use and hunting rights. I've often read that ecclesiastical lords were seen as worse, but this rarely comes with documentation so I can't confirm that firsthand.
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I'm sorry, this is not my best-organized answer...let's just say it recapitulates power politics in the medieval Holy Roman Empire. :)
A surprisingly readable source on this topic that actually addresses bishop-lords and lay-lords is Benjamin Arnold, Princes and Territories in Medieval Germany. If you want to talk about lordly violence, Thomas Bisson is your guy, but...okay, reviews of TB's books are your target. Those are some bricks. And TB--following the sources--is generally more concerned with the Church as speaking out against lordly violence rather than perpetrating it (although I got the Hugh of Langres bit from him).
I will do more research on this and come back to you, but my first rough answer would be "no".
It is important to notice that church ownership of land varied widely: church might be owned by parished, monasteries, abbeys, bishoprics, archbishoprics, holy order, lay orders etc... Everyone had to pay church tithes (not only peasants) but as far as I know these taxes weren't very different from those a lord would impose on their subjects.
For know, bare in mind this: medieval administration was incredibly diverse. More often than not, how peasants were treated depended more on the specific lord (or clergyman) at that moment rather that a general church vs secular difference. Corrupt bishops, that often came from nobility, were likely to rule as any other lord. More spiritual figures, such as lowborn clergy, abbots and abbesses were more kind-hearted.
