Biggest Winners and Losers In Padres’ Farm System In 2026

With the Minor League Baseball season starting to wrap up, now feels like a good time to zoom out and look at the San Diego Padres’ farm system as a whole.

There was a lot of action across the organization this year, whether it was prospects making their way to the major leagues, players being moved at the trade deadline, or young players taking another step in their development. Some players and teams took advantage of their opportunities, while others struggled to find the consistency they were looking for. So with that, let’s take a look at some of the biggest winners and losers from the Padres’ farm system this year, starting with the winners.

Padres' Biggest Farm System Winners (2026)

The biggest winner, in my opinion, has to be the Padres’ Single-A affiliate, the Lake Elsinore Storm. The Storm dominated over the first half of their season, finishing with a 39-27 record. That was good enough to win the California League South Division and earn a spot in the postseason, putting Lake Elsinore in position to make a run at a championship. Things didn’t go quite as smoothly during the second half of the season, but the Storm managed to rally when it mattered most. They won their first round matchup against the Dodgers’ Single-A affiliate, the Ontario Tower Buzzers, and toppled San Jose to win the California League for the fifth time in franchise history.

Considering how the second half played out, it's amazing that the Storm were able to rally to win the title. Lake Elsinore put themselves in a great position during the first half, and when the pressure ramped up in the postseason, the Storm found a way to deliver. That makes them an easy choice as one of the biggest winners in the Padres’ farm system this year.

The other big winner for me is outfield prospect Alex McCoy. McCoy began the season outside of Padres Mission’s top 20 prospects, but he has completely changed his standing within the organization over the course of the year. He currently sits at number eight on that list, and it’s easy to see why after looking at what he accomplished. Across 123 games between High-A and Double-A, McCoy produced 51 extra-base hits and 24 stolen bases while posting an .822 OPS. That’s a pretty impressive combination of power and speed, especially for a player who entered the season without much prospect recognition. 

There are still some bat-to-ball concerns that McCoy will need to work through. His strikeout tendencies are something worth monitoring as he continues to climb the minor-league ladder, and that could ultimately determine how much of his offensive production carries over against major league pitching. But man, if he can get those concerns even slightly under control, the tools are there to eventually make a difference at the major-league level. Going from outside the top 20 prospects to number eight in the span of one season is a pretty significant jump, and McCoy has given the organization another interesting young outfielder to keep an eye on moving forward.

Padres' Biggest Farm System Losers (2026)

As for the losers, we’re going with the Padres’ High-A, Double-A and Triple-A affiliates. Unlike Lake Elsinore, it was not a particularly good year for Fort Wayne, San Antonio or El Paso. The three levels collectively went 173-229, and none of them qualified for the playoffs.

Obviously, there is some context needed here. Some of those struggles can be attributed to the players San Diego traded away around the deadline, which naturally changed the makeup of several of these rosters. There are also going to be plenty of ups and downs at the minor=league level as prospects move between teams and organizations try to balance development with winning. But regardless of the reasoning, it still wasn’t a good year for any of these three affiliates.

When your Single-A affiliate is making a deep postseason run while the three levels above it all miss the playoffs, that’s certainly an interesting contrast. It doesn’t necessarily mean the Padres’ farm system is in bad shape, but it does show that there were some clear struggles once you got beyond Lake Elsinore.

The other loser I’ll mention is Padres pitching prospect Jagger Haynes. This was supposed to be an important year for Haynes, but the performance simply wasn’t there. He opened the season as San Diego’s number six prospect, but he currently sits at number 13.

Haynes posted a 4.37 ERA at Double-A San Antonio, but that number jumped all the way to 6.55 once he was promoted to Triple-A. The promotion itself is obviously a good sign, as the Padres still believed he was ready for the challenge, but the underlying numbers took a pretty sharp step backward. His strikeout rate dropped to just 17.5%, while his walk rate hovered around 12%. Across both levels, his overall strikeout-to-walk ratio finished below two-to-one, which is not the kind of performance you want to see from one of your organization’s top pitching prospects.

That doesn’t mean Haynes should suddenly be written off. He’s still fairly young and will turn 24 this weekend, giving him plenty of time to figure things out. Pitching development is rarely a straight line, and a difficult season can sometimes be part of the process. Still, this wasn’t the year the Padres wanted from Haynes.

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