Should I seperate the rooster and hens?

I have 6 pullets plus the Roo. I know people say it's ok to eat the fertile eggs and no difference but I personally am grossed out by the idea and can't get past it. Sorry!
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Don't be sorry. It is what it is. However, grossed out as you may be, there is no difference between them. People have been eating fertile chicken and other species eggs for about a million years. It's just in the last 100 years that commercial farming has brought store eggs that aren't fertile.
Whole Foods and Trader Joe's sells fertile eggs because some people prefer them.
Much like your gross out is unfounded, their thought that they are somehow better is also unfounded. An egg is an egg whether a rooster was present or not.
An egg is the same thing as a mammals' ovulation cycle.
 
You can separate him and give him a bachelor pad if you really want to keep him, but they are flock animals and he will be lonely. No I would not coop him with only 1 hen, he may over mate her causing stress, lots of visible feather damage and possibly injuries. If you really don't want fertile eggs, your best option is really to find him a new home. But as it was pointed out there is no difference in the eggs and it would take at least a few days of a hen sitting on eggs before there would be noticeable growth in a fertile egg. I mean really other then seeing then mate you wouldn't even know a fertile from an unfertile. But either way I don't have and can't have a rooster. And if and when i cam have a rooster i will not get a rooster unless I know I will be willing and able to butcher extra chickens, incase we have or let a hen hatch eggs. Because to many roosters are not good for the flock.
we have 2 roosters, a bantam and an araucana. the araucana came in a trio and the hens were a bit bare backed when we got them.
initially we had 2 buff orpingtons, but one was sick and died, my sister then got a trio of frizzy bantams, one laying and one still young, the laying hen decided she wasnt going to lay in the coop, and was seen returning into the run on many occasions, i then found 6 eggs in a pile of stones in the garden, then one day when out, she met the dog who wanted to play, down to one young bantam. we then got 3 more large fowl and all was good. just over a week later we got the trio of araucana and put them in the coop, the cock came into the garden after about 20 minutes and was jumped on by the bantam rooster, obviously the outcome was inevitable and after a bit of chicken kungfu, the bantam was chased off. since then they have not been any bother to each other, the bantam tries to mate with all the hens and the big cock just isnt bothered by it, personally im not sure he can actually complete the deed,
in the last few weeks ive been noticing more damage to the araucana hens, so much that i can see the wing joint, and one is starting to lose neck feathers, i think this maybe due to the bantam hanging on for life as the hens run off,
so heres the idea, i have just fenced of a section the whole length of the run and built a 2foot pitched roof box off the floor with a perch, the idea is to segregate the males allowing one day a week access to the hens, at least until winter when we will allow them back into the flock permenantly or at least through winter. the bantam hen can squeeze through the fence but the cock cant, for us this is ok coz the araucana rooster does not bother her. i have also halved the gaps in the perimeter fence round the patio as the hen just started laying and she too wanted to lay outside the run so now. can not get out and has started laying in the coop, but she is usually led and accompanied into the coop by the little cock,

will it be a problem removing the cocks into the separate area and will it be ok to allow weekly access?
the fence has been open and up for over a week, all the flock is now used to going through the gap into both sides, and all have been building inspectors during the roost construction.
2 of the hens have actually been inside before completion but i havent seen the cocks in it yet.
when they are segregated would i need to put them in the roost and lock them in or allow them to work it out for themselves?
 
2 roosters just depends on if they will decide to get along or not, many will fight to the death if allowed. As for the setup from other posts I've seen that's the most ideal. They are side by side and therefore still part of the flock but separate to reduce stress on the girls. Good job

we have 2 roosters, a bantam and an araucana. the araucana came in a trio and the hens were a bit bare backed when we got them.
initially we had 2 buff orpingtons, but one was sick and died, my sister then got a trio of frizzy bantams, one laying and one still young, the laying hen decided she wasnt going to lay in the coop, and was seen returning into the run on many occasions, i then found 6 eggs in a pile of stones in the garden, then one day when out, she met the dog who wanted to play, down to one young bantam. we then got 3 more large fowl and all was good. just over a week later we got the trio of araucana and put them in the coop, the cock came into the garden after about 20 minutes and was jumped on by the bantam rooster, obviously the outcome was inevitable and after a bit of chicken kungfu, the bantam was chased off. since then they have not been any bother to each other, the bantam tries to mate with all the hens and the big cock just isnt bothered by it, personally im not sure he can actually complete the deed, 
 in the last few weeks ive been noticing more damage to the araucana hens, so much that i can see the wing joint, and one is starting to lose neck feathers, i think this maybe due to the bantam hanging on for life as the hens run off, 
so heres the idea, i have just fenced of a section the whole length of the run and built a 2foot pitched roof box off the floor with a perch, the idea is to segregate the males allowing one day a week access to the hens, at least until winter when we will allow them back into the flock permenantly or at least through winter. the bantam hen can squeeze through the fence but the cock cant, for us this is ok coz the araucana rooster does not bother her. i have also halved the gaps in the perimeter fence round the patio as the hen just started laying and she too wanted to lay outside the run so now. can not get out and has started laying in the coop, but she is usually led and accompanied into the coop by the little cock,

will it be a problem removing the cocks into the separate area and will it be ok to allow weekly access?
the fence has been open and up for over a week, all the flock is now used to going through the gap into both sides, and all have been building inspectors during the roost construction.
2 of the hens have actually been inside before completion but i havent seen the cocks in it yet.
when they are segregated would i need to put them in the roost and lock them in or allow them to work it out for themselves?
 
night 1
went into the coop after they all went in and took out the araucana cock and put him in the roost, went back got the bantam cock and put him in the roost and blocked them in, all was quiet, they slept on the floor,
day/night 2
let them out at 10.30 am bantam runs out in seconds, araucana poked his head out after a few minutes and came out slowly. both spent a few hours pacing the fence, mainly at where the access through was. at dusk, roosters get agitated and start pacing the fence quicker as the hens retire to the coop, araucana manages to jump onto the lowest part of the fence bordering the patio, 20 minutes of chase the rooster ensue, meanwhile the bantam goes up the ramp but does not enter, we manage to catch the araucana and transport him into the roost, he does not come out, 5 mins later the bantam goes in, they sleep on the floor (door left open)
day/night 3
i go out at 8am, both cocks are in a small group with half the 5 week old chicks, the food bowl is in a hole so they can all feed by it together, i throw some feed at the fence border so the can mingle. the bantam hen is in and out the cocks area all day as are the 6 chicks. the bantam cock retires early and jumps up onto the perch, the araucana goes up the ramp to inspect 3 times but doesnt go in. he gets agitated walking the fence as the hens retire to the coop but does not attempt to jump the fence, he then goes into the roost and jumps on the perch, the bantam comes out for 5 minutes and then returns,,,,,,,,,,,,
all is good with the world...
the bantam no longer tries to large it over the chicks and the araucana seems to be more helpful towards them, i guess the chicks actually feel more safer on the cocks side (no hens putting them in their order or chasing them off) and the cocks seem glad of the company.
 
night 1
went into the coop after they all went in and took out the araucana cock and put him in the roost, went back got the bantam cock and put him in the roost and blocked them in, all was quiet, they slept on the floor,
day/night 2 
let them out at 10.30 am bantam runs out in seconds, araucana poked his head out after a few minutes and came out slowly. both spent a few hours pacing the fence, mainly at where the access through was. at dusk, roosters get agitated and start pacing the fence quicker as the hens retire to the coop, araucana manages to jump onto the lowest part of the fence bordering the patio, 20 minutes of chase the rooster ensue, meanwhile the bantam goes up the ramp but does not enter, we manage to catch the araucana and transport him into the roost, he does not come out, 5 mins later the bantam goes in, they sleep on the floor (door left open)
day/night 3
i go out at 8am, both cocks are in a small group with half the 5 week old chicks, the food bowl is in a hole so they can all feed by it together, i throw some feed at the fence border so the can mingle. the bantam hen is in and out the cocks area all day as are the 6 chicks. the bantam cock retires early and jumps up onto the perch, the araucana goes up the ramp to inspect 3 times but doesnt go in. he gets agitated walking the fence as the hens retire to the coop but does not attempt to jump the fence, he then goes into the roost and jumps on the perch, the bantam comes out for 5 minutes and then returns,,,,,,,,,,,,
    all is good with the world...
  the bantam no longer tries to large it over the chicks and the araucana seems to be more helpful towards them, i guess the chicks actually feel more safer on the cocks side (no hens putting them in their order or chasing them off) and the cocks seem glad of the company.
sounds like you found a good set up for your boys
 

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