Updated: Dec 25, 2022
This question is one of the main perplexities in spirituality for every spiritual ever… This is one of the main challenges a spiritual seeker meets along his spiritual path. Religions and ancient spiritual traditions came with various answers about it, and in the following I will share with you my experience when I stumbled upon the same issue.
How to know if messages are coming from your mind or your Soul?
Each spiritual walking the Path wonders quite often if what he/she gets by messages, dreams, visions, apparent synchronicities, etc., is real guidance coming from his soul or spiritual guides, or just coming from his mind and ego.

Factors that influence the source of a message
There is no easy answer to discern between the message sources, and from my research the difference between the typical self-deluded spiritual thinking that the majority of what he feels or receives as messages is guidance from his soul or some other higher entity, and a truly advanced seeker is given by following factors:
how much practice in an advanced type of meditation does the seeker have
how many limiting beliefs he released until then from his subconscious,
how good he is in shifting his awareness from his mind into his heart in order to connect with his soul
if he has access to true higher souls to check and calibrate with them
how sensitive to energies he became by practice, so he reached spiritual discernment
how humble he is
If the spiritual seeker is advanced in all of the above he necessarily will also have a more advanced soul with at least a 4.5 vibration (awareness level on the chakra scale), and a body close to 4.0 vibe or more also on the chakra scale, while average people are about 3.5 vibe both soul and body on chakra scale.
Vibration level influences the discernment ability of a person
A higher vibration level (awareness actually) both for soul and body will give anyone a higher discernment ability in telling which are body/ego feelings and which are messages from his soul. Therefore, a truly advanced spiritual will be able to discern with over 70% accuracy if the message comes from his ego or soul.
Another point I want to stress: some small level of ego is ok, it’s actually necessary on this planet and level of 3D humanity, as long as it doesn’t get inflated; one just needs to keep it under control. It’s nonsense when someone says one should completely erase his ego, it means he doesn’t understand just about anything about spirituality and energy mechanics in Creation. Without the ability to be assertive for instance, how else can a seeker keep some personal space so as to be able to make choices and progress?
Method to discern the answer from ego vs. your soul
There is no certain trick or hack to be applied by the armchair spiritual to differentiate between the two. One thing is theory and another thing is practice, we should not get lost in spiritual theories and disregard practice, that is if we want to really progress on the Path...
Nonetheless, as a general rule of thumb, if you want to find the answer to some life-important questions for you, I advise you the following method:
Do first meditation and breathwork so to raise your body vibration some, and distance yourself from the lower vibrational environment around you.
If you use in your practice other awareness growth procedures do use them. They can be sacred music, sacred dance, asanas, etc.
When you feel relaxed, at peace, and balanced inside, with your eyes closed, ask your question. It must be a question you don't already know the answer to, like "Should I marry this person?", "Should I accept this job offer?", etc, not something mundane like "Should I go and fix my car?"
The answer that comes to you in less than 3-4 sec is the answer you were looking for. If it takes longer chances are your mind had time to concoct an answer based on your beliefs and served it to you.
All the preparation before asking the question is actually aiming to open a secure and clean channel between your mind and your soul, or even to your parent-soul or spiritual guides, who have a much higher knowledge than us.
Moreover, to increase accuracy, one can do several sessions of calibration before asking important questions, where I advise asking somebody to help you, so have an external independent reference.
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You can learn more by reading other posts in this spiritual site that are coming from a very different and fresh angle than spiritual mainstream, and based on a very long and personal experience and hands-on research, and not from books.
You might also consider a service like Psychic Readings in the Services section of this site from the ones listed there and get a spiritual diagnostic, or attend my spiritual School of Body and Soul Ascension Mastery so to raise your body and soul awareness, and reach into higher dimensions.