Minecraft Edition

Minecraft is available in two separate editions, Java Edition and Bedrock Edition. While Bedrock Edition has a higher raw player count, Java Edition is often a better choice for running a server as the player base is more mature and more likely to connect to multiplayer servers. It’s also possible to allow Bedrock players to connect to Java servers using third party software. Check out this article for an in-depth overview of all the pros and cons, as well as how to allow Bedrock players to connect to a Java Edition server.

The information linked from this guide has an inherent bias towards Minecraft Java Edition due to my significant familiarity with it over Bedrock, so almost all the information provided here is most beneficial to Java Edition server administrators. Due to this I’d personally recommend running Java Edition, possibly with GeyserMC to allow Bedrock players. If you do choose to run Bedrock Edition the following information will likely not be as relevant to you as it would be for Java Edition. That’s not to say it’s the wrong choice; this is just not the right guide for you if that’s a choice that makes sense for your situation.

Minecraft Version

On Minecraft Java Edition, players can fairly easily choose what version of the game to run. This means that server owners can set up servers that target specific niches of players that prefer older versions. This guide goes over many of the reasons why you should run the latest version of the game. While it is still possible to run servers for old versions, due to the reasons outlined in the linked article, it can be a significantly larger undertaking.

Server Software

Almost every public Minecraft server is custom in some capacity. While running the official Minecraft server software is possible, you’d be missing out on significantly better admin tools, gameplay customisations, and performance improvements. Minecraft’s official data pack system has come a long way and can provide some level of customisation, it’s still magnitudes behind custom server software, and often best used alongside plugins or mods.

Plugins

If you've decided to use a Bukkit-based server, you'll very quickly notice just how many plugins are available. If you’re using Spigot, the official plugin site is Spigot Resources, and for Paper the official site is Hangar. The original Bukkit plugin site, BukkitDev, also still hosts many plugins, and Modrinth hosts plugin while remaining unaffiliated to any specific server software project.

If you're looking for general advice on what plugins you should get, check out this top 10 list of most useful plugins for the average Minecraft server. If you're looking on Spigot resources or a handful of other sites, you may notice that some plugins have a price tag. It’s worth noting that paying for plugins is not a requirement to run a Minecraft server but can sometimes make sense for your specific circumstances. This articles goes into more details on paid plugins..

Some plugins offer a selection of features, such as EssentialsX or CraftBook, while others provide a single feature. There are some disagreements throughout various parts of the server owner community about whether these larger plugins are a good idea or not. This article discusses how to make the best choice around using large plugins with many features or multiple small plugins that offer single features.

When configuring plugins, often, you'll have the option of using MySQL or some other form of database. Check out this guide on how to make the best decision regarding data storage. No one single form of data storage is the best in all situations, and they all have their various pros and cons. Making the wrong decision here can significantly impact performance and increase the possibility of data loss.

Performance

If you're having performance issues, the first thing you should always do is make sure you're using Aikar's optimised Java flags. Aikar frequently updates this guide to ensure that the flags are up to date for modern Minecraft servers and provide the best performance. These flags tune Java’s internal settings to best suite the Minecraft server.

Celebrimbor on the Spigot forums has created a guide on optimising Minecraft servers and provides a thorough look at many of the various configuration options that both Paper and Spigot provide. Check out his guide here.

If you're still having performance issues, this guide goes over how to properly use the Timings system built into Spigot to identify the source of the problem.

Quite often, when encountering performance problems, server owners might add plugins that claim to reduce lag. These plugins are almost always a bad idea and generally produce more lag than they could ever possibly solve. A recent form of plugin that's popped up is mob stacker plugins. You should not use these plugins, and this article explains why. If doing something like this improved performance, it’d be integrated into Paper itself.

Plugin Issues

Issues on your Minecraft server that you can't find the cause of are often frustrating. For general issues, this guide covers a few techniques to help find the cause of the issue.

One semi-common category of plugin issues are plugin conflicts. These arise when two plugins do something that just don’t work well together. Sometimes these are due to a problem in one of the plugins, and other times it’s just a case of two inherently incompatible behaviours, such as a plugin that lets pigs fly and another that forces pigs to live underwater. This article explains what plugin conflicts are and what you can do about them.

No matter what type of issue it is however, once you’ve narrowed down the plugin causing the problem you should reach out to the plugin’s developers. Asking in a generalised support forum or chat room is often slower and won't provide accurate answers, but can still be useful in cases where developers don’t have dedicated support channels. In saying that, most server plugins have support Discords or forums that will happily field your questions and problems. Worst case, asking the support of your server platform, such as Paper, can be a good way to deal with tougher issues. Check out this guide on how to best ask for support from open-source software projects.

Host Issues

Sometimes issues can be caused by your Minecraft server host and can therefore only be resolved by them. Check out this article on a few of the various issues that often pop up with Minecraft server hosts.

Do not /reload

If you're running a Bukkit-based server, you may have noticed the /reload command, or other plugins such as PlugMan that allow reloading individual plugins. While convenient, you should never do this. This article explains why. If you encounter an issue and you've used /reload or similar, always restart the server to see if the issue still occurs. In general, always restart the server instead of using reload commands.

Importing builds

If you're downloading Minecraft builds to add to your server or have hired a build team, you've likely seen files that end in .schem or .schematic. These are schematic files and are loaded using the mod and plugin WorldEdit. Check out this guide on how to work with these files.

Security

If your server is public, security should be one of your highest priorities. MrDienns of Dyescape has written a fantastic guide on how servers get hacked and how to protect yourself. Check it out here.

In recent years, the most common attack vector for servers has become plugin-based malware. These take the form of malicious plugins, that oftentimes infect other installed plugins and the server software itself, making it harder to remove. This article covers Minecraft Malware and what to do about it.

One key mistake that many new server admins make, and even some server hosts, is running the Minecraft server as the root user or with administrator privileges. This significantly increases the amount of damage that a malicious actor or piece of software can actually do. Read more about the dangers of running a Minecraft server as root here.

Keep up to date

If you're operating a larger Minecraft network, keeping up to date with the download links for projects such as Paper, Velocity, Waterfall, Geyser, and Floodgate can be a hassle. You can bookmark link aggregator sites such as this one to access download links for all of these projects from a single page.

It’s important to note that sites providing actual download jar files, rather than just collating links to the official downloads, are a bad idea. The previously linked site aggregates different links in one place, but you’re still downloading from the official sources. Other sites, especially those that host Spigot jar downloads, are providing non-official copies of the software. While some may be safe, this is still potentially dangerous and can lead to malware infections.

Upgrading your server

An oft-debated question in some parts of the Minecraft server space is whether you should run the --forceUpgrade flag when upgrading to a newer version of Minecraft. Proponents will claim it makes the server run faster, while detractors will cite the various problems this can cause. This article covers the pros and cons, and what you should do in your situation.