Yes certainly it will.
First before i tell you why you need to understand the following:
In order for muscles to grow you need a lot of energy that comes from carbs in addition to protein. Many skinny guys who focus on protein only never see their muscles growing because of not providing enough energy. (see Why don't my muscles show)
Since you would never know the exact amount of energy needed the safest practice is to provide more than needed just in case. That's why eating a lot of carbs is one of the keys to muscle growth.
When you run a lot you consume a lot of energy that should have been saved for muscle growth especially if you were a skinny guy with a fast metabolism (ectomoprh , See How can ectomoprhs get bigger).
So running consumes the energy needed for muscle growth and so growth is hindered.
In addition if you run a lot in such a way that you consumed all availble carbs your body will break down your muscles for energy!!! So running can either directly reduce muscle mass by breaking down muscles or indirectly by consuming the energy needed for growth.
Your body has three types of muscle fibers, fast twitch, slow twitch and intermediate fibers. Slow twitch are the fibers that provide energy for prolonged periods like when you are running and those fibers barely grow.
Fast twitch fibers provide short bursts of high energy that are used when you lift heavy weights for few seconds.
Intermediate fibers can either turn into fast twitch or slow twitch fibers. Now when you run a lot or do cardio you actually convert intermediate fibers to slow twitch fibers instead of fast twitch and so hinder your muscle growth!!!!!
So in short, in order to grow your muscles you need to reduce cardio and running as much as possible especially if you were a skinny guy.
I have spent years doing the wrong things in the gym and didn't get any results, fortunately i came across the book No nonsense muscle building which helped me get rid of most of the misconceptions that i had about body building and guided me to the right way that a skinny guy should follow in order to get bigger, its worth checking out.
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