Follicular Phase Seed Cycling Cups: Days 1-14 (Paleo)

8 minute read

These “nutty” and chocolate-y seed cycling cups are a delicious way to support your hormones, naturally! As a Nutritional Therapy Practitioner, I am always doing what I can to support my body in a more holistic and natural way and seed cycling is one of them. When I was dealing with a lot of the chronic symptoms of my Hashimoto’s, my cycles became very very short and I dealt with a lot of PMS symptoms like acne, mood swings, irritability, fatigue, sleeplessness, and cramping.

Within the first month of starting seed cycling, my cycle went from 20 days to 27, and all of my PMS symptoms either completely disappeared or drastically lessened, I couldn’t believe it! Now, it has been several months and I have to say, I will continue doing this for the rest of my life as all of my symptoms have gone away and my cycle is so much more balanced. These amazing and delicious seed cycling butter cups make it so tasty and easy to start seed cycling today!

What is Seed Cycling

Seed cycling is a natural way using whole food seeds to support the delicate balance of a woman’s hormones.  When this balance becomes off balance due to diet, environmental toxins, lack of sleep, stress, exercise, medications, or illness it can lead to an array of chronic symptoms such as PMS, headaches, irregular menstrual cycles, PCOS, acne, mood swings and more. 

One of the easiest and most natural ways you can support your body’s reproductive hormones is with seed cycling.  As I have told many clients, your body is this amazing machine that has the ability to restore and heal when given what it needs.  So let’s dive into seed cycling some more!

How does Seed Cycling work to Balance Hormones in the Follicular Phase

The first 14-days of a woman’s cycle begins the day her period starts, this is considered the follicular phase and is when a woman’s body is working to build up the endometrium (uterine lining).  This phase of a woman’s cycle is more estrogen dominant and seeds such as pumpkin and flax support the body’s estrogen levels due to the phytoestrogens that are found in the seeds.  The lignans found in flaxseeds help to support the body’s estrogen levels by preventing excess estrogen by binding to it, while pumpkin seeds are high in zinc, a mineral that is necessary in progesterone production in the luteal phase (days 15-28) of your cycle. 

There are other health benefits to including flaxseeds and pumpkin seeds to your diet!  To learn about the Luteal Phase, sunflower seeds and sesame seeds, check out my Luteal Phase Seed Cycling Cups: Days 15-28 HERE.


Omega-3’s: An essential fatty acid that is necessary in the body’s anti-inflammatory pathways

Fiber: There are more benefits to eating the flaxseeds, they are full of fiber to support a healthy and optimized digestive tract! They contain both soluble and insoluble fiber:

  • Insoluble fiber: Works to keep things moving along and helps with toxin and waste elimination.
  • Soluble fiber [1]: Soluble fiber works to support a healthy microbiome and supports healthy blood sugar regulation.


  • Vitamin B1 (thiamine): A water soluble vitamin that is essential in glucose metabolism and supports health heart and nervous system function.
  • Vitamin B6: A water soluble vitamin that is essential in metabolic pathways,  RBC production, and in the production of neurotransmitters.
  • Vitamin B9 (folate):  A water soluble vitamin that is essential during pregnancy in the formation of the neural tube [2].


  • Copper:  Essential mineral in the formation of red blood cells and in supporting cardiovascular health and immune function [3].
  • Iron: Necessary in the formation of hemoglobin and maintaining proper body temperature.  Plant sources of iron and are considered non-heme, which is not as easily absorbed, pairing non-heme iron rich foods with foods rich in Vitamin C increases absorption.
  • Manganese: Essential mineral in supporting blood sugar regulation, glucose metabolism, and supporting healthy brain and nerve function [4].
  • Magnesium: The fourth most abundant mineral in the body, it support healthy nerve functions, healthy blood pressure, and detoxification.
  • Phosphorus: Supports healthy teeth and bones, muscle recovery after working out, and detoxification.
  • Selenium: Supports thyroid health [5] and supports your immune system.
  • Zinc: Essential in digestion, thyroid health, and a healthy immune system.

Pumpkin Seeds

Pumpkin seeds are a great source of protein, which is the source of the amino acids your body needs for every function that support you from immune health to the synthesis of hormones.  Pumpkin seeds contain all nine essential amino acids, making this one of the few complete plant protein sources you can find [6].

Vitamins:  You will find Vitamin K1, which is essential in supporting your body’s ability to clot.  Vitamin K1 is converted to vitamin K2 by your microbiome, which helps to support your bones health, brain and heart health [7].

Minerals: Full of essential minerals that support many of the functions and processes in our bodies, these include Copper, Manganese, Magnesium, Phosphorus, Iron and Zinc. 

What are the Benefits of Seed Cycling*

Seed cycling can have a positive impact on various symptoms of hormonal imbalances in as soon as a few weeks to months after starting including

  • Hormonal balance
  • Reduction in PMS symptoms: bloating, cramping, headache, mood swings, sugar cravings, fatigue
  • Improving and regulating your cycle and flow
  • Can help stimulate menstruation if absent
  • Supporting fertility
  • Improving symptoms associated with PCOS, ovarian cysts, fibroids, and endometriosis
  • Improved libido
  • Improved sleep
  • Improves symptoms during peri-menopause and post-menopause

* There is not a lot of scientific data that supports these claims, however, there are many testimonials, mine included, that support seed cycling and its benefits.

How to Start Seed Cycling

Seed Cycling is one of the easiest ways to add more nutrients to support a healthy hormonal balance.  During the follicular phase (days 1-14), you will eat 1 Tablespoon each of pumpkin and flaxseeds each day.  During the luteal phase (days 15-28), you will eat 1 Tablespoon of each sunflower and sesame seeds each day. 

Days 1-14: Follicular Phase, starts the first day of your period

  • Eat 1 Tablespoon of Pumpkin Seeds: ground
  • Eat 1 Tablespoon of Flaxseeds: ground

Days 15-28: Luteal Phase

  • Eat 1 Tablespoon of Sunflower seeds, ground
  • Eat 1 Tablespoon of Sesame seeds, ground

Seed Cycling FAQs

Q: When should I start seed cycling?

A: If you are menstruating, start on the first day of your next period.  If you are peri-menopausal or post-menopausal and are experiencing amenorrhea, start with the seed cycling anytime you like and follow the timeline of the 14-day rotation.

Q: What if my cycle is shorter? Longer?

A: Not everyone has a cycle that is 28-days, many of us are less than that and many of us are longer.  Everyone is different, and that’s okay.

If you cycle is shorter than 28 days like I was, then stop the luteal phase seeds and restart the follicular seeds when your period starts. Over time you may see improvement in the cycle length. If you have consistently shorter cycles, you may also decrease the number of days you are in each phase, for instance, if you have a 26-day cycle, you can choose to do each phase for 13 days instead of 14.  Listen to your body, you know what is best for you.

If you cycle is longer, I recommend sticking with the 14-day cycling as close as possible to help provide the necessary nutrients in supporting the body’s natural hormonal balance of a 28-day cycle. 

Q:  Do the seeds have to be ground?

A: Grinding the seeds helps to improve the availability of the nutrients in the seeds by breaking the seeds down into a more absorbable form.  You can grind them up in a coffee grinder, food processor, or blender and add them to different foods or make seed cycling cups to enjoy. 

Q: What if I can’t eat certain seeds?

A: Try to add the ones you can during the specific phases they support, and avoid flax and pumpkin seeds during your luteal phases and sesame and sunflower during your follicular phases.

Q: What if I don’t have time to ground fresh seeds everyday?

A: There are so many alternatives!  Make seed butter cups like I do and keep them in the fridge/freezer, make your own seed powder or seed butter to add to other foods, or even just buy organic seed butters (what I do A LOT) and eat a Tablespoon of each on some celery, apples, or toast!

Q: What are some other ways to add the seeds to my diet?

A: So many answers here, but I’ll throw these out!

Paleo Seed Cycling Cups Days 1-14

Makes 14-16 mini-cups*

2 cups Raw Pumpkin Seeds or Pepitas OR 1 cup of Pumpkin Seed Butter

1/4cup-1/2 cup of a neutral oil: Avocado, MCT oil**

3/4 cup Ground Flaxseed

2/3 cup Hu chocolate or 70% or higher dark chocolate, melted

1/2 tsp Pure Vanilla Extract (opt)

1-2 dropper fulls of Pure Organic Stevia (opt) OR 1-2 Tbsp Pure Maple Syrup or Honey

1/2 tsp Ground Cinnamon (opt)

Pinch of sea salt (opt)

Cacao Nibs for topping (opt)

Flaked Sea Salt for topping (opt)

Pumpkin seeds for topping (opt)

*This recipe makes about 1/2 cup more of pumpkin and flaxseed butter mix that I love to add to my smoothies, and use as a delicious seed butter for apple slices and celery stick during my follicular phase.

** Omit the oil if you are using a pre-made pumpkin seed butter

How to Make Paleo Seed Cycling Cups Days 1-14

1.  Melt the chocolate over a double boiler or in the microwave.

2.  Line a mini-cupcake pan with liners.

3.  Using a spoon, fill the bottom about 1/8th full of chocolate and freeze for 10-15 minutes while you make the pumpkin seed butter mixture. 

4.  Add the pumpkin seeds/pepitas to a blender and blend on high. 

5.  Drizzle in the Avocado Oil or MCT oil into the blender as it’s making a pumpkin seed butter.

6.  Transfer the pumpkin seed butter to a medium bowl and add the ground flaxseed.

7.  Add any whole food sweetener or spices you like and mix well until evenly combined, set aside.

8.  Take the cupcake tin out of the freezer and add 2 Tbsp of the pumpkin seed butter mixture to the liner, it should fill it up to the top.  Freeze for 60-minutes until the tops have mostly hardened.

9.  Drizzle the remaining chocolate over the top of the seed cycle butter cups and top with anything else you like: flaked sea salt, cacao nibs, pumpkin seeds, flaxseeds

10.  Freeze for 2-4 hours until firm.

11.  Transfer to a freezer safe container or freezer bag and enjoy 1 seed butter cup every day during your follicular phase.

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Q: Can I keep these in the refrigerator so they aren’t as solid?

A: Absolutely! I just like to keep my frozen to keep the pumpkin seed butter from running. If you are going to keep them in the fridge, I would opt for a container you could stack them up.

Q: Can I use whole flaxseed in this recipe?

A: Yes, you can! Just grind it first so you can maximize the absorption of the nutrients!

Q: What if I have left over filling?

A: You can do a few things with it, I love to use any leftover seed butter filling to eat with apple slices, celery, on a sandwich, to add to smoothies or oatmeal, or just to eat by the spoonful! OR, you can make extra cups and save them for the next luteal cycle.

Note: This post contains Amazon affiliate links to the products and kitchen gear I love. If you click on a link and make a purchase, I receive a small commission at no cost to you. Thank you for supporting Almond Milk and Cookies!


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Welcome to Almond Milk and Cookies where good food, health and lots of flavor go hand-in-hand!

I am a holistic nutritionist with an auto-immune disorder, a love of cooking, and a passion for holistic health.

Sharing what I make and eat with all of you…in hopes that you find inspiration here to fuel your body and feel your best with nutrient dense whole foods and clean eating.

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