With growth comes growing pains, even for the top pitching prospect in baseball.

Pitching on four days' rest for the first time as a professional, Paul Skenes allowed his first home run since the Pirates selected him with the No. 1 overall Draft pick last July, but he limited the damage and helped lead Triple-A Indianapolis to an 8-3 win over Buffalo on Sunday.

"The biggest thing is just the learning experience of it all," said Skenes regarding pitching on four days rest. "Doing the five day is a little bit different, so [I'm] just trying to figure out the routine of it and getting used to it."

The home run, a solo shot in the fifth from Bisons outfielder Will Robertson, was one of two runs Skenes allowed on the day over 4 1/3 innings, but so dominant has the 6-foot-6 right-hander been this year that the performance only raised his season ERA to 0.99 over seven Triple-A starts. Skenes, who surrendered two knocks and a walk in the first frame, finished his start with three hits, two walks and four strikeouts, throwing 66 pitches, 40 for strikes.

MLB's No. 3 overall prospect has allowed just four runs -- three earned -- on 17 hits and eight walks over 27 1/3 Triple-A innings on the season, striking out 45 along the way.

After giving up a run in the first Sunday, Skenes found his groove, breezing through the next nine Buffalo hitters without allowing a runner on base. In the fifth however, the Bisons tacked on another run against the former LSU Tiger -- with help from a challenge that went against them.

• MLB Pipeline | Top 100 prospects | Prospect video

On a 3-1 count to Robertson, who was leading off the fifth for Buffalo, Skenes painted in the inside corner with a 98.6 mph fastball, but the pitch was called a ball, leading Indy catcher Grant Koch to challenge. The replay revealed that the pitch clipped the strike zone. After Robertson reattached his shin guard and returned to the plate, Skenes served up his second-slowest fastball of the season (97.9 mph) and Robertson sent it 421 feet over the wall in center for his sixth homer of the year.

Skenes' velocity was noticeably down in the inning, with his four slowest four-seamers of the season coming in a five-pitch span against the final two batters he faced before he was lifted. The big righty rebounded from the home run to retire the last batter he faced on a grounder to third.

Skenes did still eclipse 100 mph with his fastball on nine pitches in the outing, with the pitch averaging 99.3 mph, the second-lowest mark in his seven starts. He also threw 61% of his fastballs for strikes, the lowest strike rate with his heater so far this year.

"It was a little bit inconsistent," Skenes said about his execution in the zone. "Early in the game it was really good, late in the game I kind of started laboring a little bit. Maybe trying too hard on certain pitches, but I think it was good overall."

Execution is the 21-year-old's only goal on the mound, to "throw the right pitch in the right spot at the right time."

• Subscribe to the MLB Pipeline Newsletter

With Skenes' pitch counts rising and his success stacking up, fans are hoping to see the flame-thrower in Pittsburgh in the near future, but he doesn't let the outside hype affect him.

"All that is cool, but it's just noise," Skenes said. "[I] got to get back to what I do well and just execute against the hitters because without that everything else goes away."