When choosing a contraceptive, we’re often told to think about side effects like weight changes, mood swings, or bleeding patterns. But there’s another factor that gets overlooked: your vaginal microbiome.With so many options out there and growing research into how they affect your vaginal health, making a choice can feel overwhelming. So, we’ve broken it down. Here’s what you need to know about how different contraceptive methods impact the vaginal microbiome – and what it means for your long-term health.
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When choosing a contraceptive, we’re often told to think about side effects like weight changes, mood swings, or bleeding patterns. But there’s another factor that gets overlooked: your vaginal microbiome.With so many options out there and growing research into how they affect your vaginal health, making a choice can feel overwhelming. So, we’ve broken it down. Here’s what you need to know about how different contraceptive methods impact the vaginal microbiome – and what it means for your long-term health.
Oestrogen plays a key role in supporting your vaginal health. It helps the vagina produce glycogen, a natural sugar that feeds Lactobacilli, which are the protective bacteria that support a healthy vaginal microbiome.
When Lactobacilli thrive, they help maintain a low pH (slightly acidic), outnumber harmful bacteria and produce antimicrobial substances to fight them off. But when their levels drop, harmful microbes can take over, leading to dysbiosis and discomfort.
That’s why contraceptives that contain oestrogen (like the pill) tend to support the microbiome, while others can trigger inflammation or suppress oestrogen, making it harder for Lactobacilli to thrive.
It’s worth noting that oestrogen isn’t always protective. In some people, high oestrogen levels can promote yeast overgrowth, since Candida also feeds on glycogen. So, oestrogen-based contraceptives can stabilise the microbiome for some, while potentially triggering thrush (Vulvovaginal candidiasis) in others.
Choosing contraception is already difficult. Adding your vaginal health into the mix can feel overwhelming. So, we’ve put together an overview of how each method might impact your vaginal microbiome – helping you make the choice that works best for your body.
If you’re using fertility tracking or no contraception, your vaginal microbiome will shift with your hormone levels across your menstrual cycle. Studies show that oestrogen fluctuations cause natural drops in Lactobacilli (especially during menstruation) and temporary surges in other bacteria.
While these shifts are normal, those with less stable microbiomes at baseline may notice more infections or irritation at certain points in their cycle. So, using no contraception isn’t harmful for your vaginal microbiome, but it doesn’t help stabilise it either.
Condoms are a hormone-free way to prevent pregnancy and protect against STIs, but they may also support your vaginal microbiome.
Semen is alkaline, so unprotected sex can raise the vaginal pH and introduce disruptive bacteria. Condoms provide a physical barrier to block semen, preserving the natural acidic environment in the vagina. In fact, one study found consistent condom use helped preserve microbiome balance and lower rates of bacterial vaginosis.
However, not all condoms are created equal. Avoid ones made with spermicide or flavoured lubricants, as these contain chemicals and sugars that can disrupt your vaginal microbiome.
The combined oral contraceptive pill (often just called “the pill”) is one of the most widely used forms of hormonal contraception. It contains synthetic oestrogen and progestin, which prevent ovulation to reduce the chance of pregnancy. But research suggests the pill may also support vaginal health.
A two-year study showed users had more stable vaginal microbiomes dominated by Lactobacilli – especially Lactobacillus crispatus and L. jensenii, two species linked to a lower risk of infection. Another study found lower rates of BV and fewer microbiome changes among pill users.
Oestrogen’s ability to boost glycogen production and help Lactobacilli to thrive may help protect the vagina from infection. While responses vary depending on hormone type and dose, the combined pill is the method most consistently linked with a stable, Lactobacillus-rich microbiome.
The mini pill (progestin-only pill or POP) delivers a low daily dose of progestin to thicken the uterus lining, slow sperm movement and in some cases, suppress ovulation. It contains no oestrogen, so it offers less support for Lactobacilli.
There are limited studies on the mini pill and the microbiome, but existing research suggests it has a mild impact. Some users maintain healthy microbiomes, while others see more bacterial diversity, potentially due to increased menstrual bleeding on the mini-pill.
Hormonal implants (like Nexplanon) are inserted just under the skin in the arm and release a continuous low dose of progestin for up to three years. They work similarly to the mini pill, suppressing ovulation and thickening cervical mucus.
Research on the implant and the microbiome is sparse, with early findings showing mixed outcomes. One study found the implant had no significant impact on the microbiome, showing the injection and copper IUD to be more disruptive.
The injection, also known as Depo-Provera, contains depot medroxyprogesterone acetate (DMPA), a long-acting form of progestin. It’s injected every 12 weeks to suppress ovulation and thicken cervical mucus.
DMPA has been shown to raise vaginal pH and reduce Lactobacilli levels, with one study suggesting DMPA may delay Lactobacilli recovery in postpartum women. However, another found it actually increased the population of beneficial Lactobacilli.
The vaginal ring (like NuvaRing) is a flexible device inserted into the vagina that releases oestrogen and progestin to prevent ovulation. Early evidence suggests it may offer similar benefits to the combined pill.
One study found that ring users had stable levels of Lactobacilli and fewer infections. However, a 2023 review warns about bacterial biofilms forming on the ring’s surface, potentially interfering with drug delivery and promoting antimicrobial resistance. More research is needed.
Hormonal IUDs (such as Mirena) are inserted into the uterus and release a low dose of levonorgestrel over time. They prevent pregnancy by thickening cervical mucus and thinning the uterine lining. In some cases, they also suppress ovulation.
Again, the research is limited with mixed findings. They’re less disruptive than copper IUDs, but still linked to reduced Lactobacilli in some cases. Some studies suggest hormonal IUDs may help reduce BV risk by lowering menstrual blood volume, which limits iron, a nutrient that can fuel harmful bacteria.
However, hormonal IUDs are not microbiome-neutral. Responses vary, and some users may still experience microbial imbalance – we need more research.
The copper IUD (Cu-IUD) is a hormone-free, long-acting contraceptive that prevents pregnancy by releasing copper ions, which are toxic to sperm. However, several studies suggest it may disrupt the vaginal microbiome.
Research links the copper IUD to higher vaginal pH, increased total bacterial load, and a drop in protective Lactobacilli levels. Users are more likely to show overgrowth of inflammatory bacteria like Prevotella and Sneathia, which are associated with BV, inflammation and higher STI risk. In vitro studies also showed that copper ions can inhibit the growth of L. crispatus, contributing to the imbalance.
This doesn’t mean the copper IUD is unsafe, but it does highlight the importance of personalised advice, especially for people prone to infection.
If you’re dealing with chronic thrush, BV or UTIs, your contraception could be an important part of the picture. Depending on your natural microbiome stability, the type of contraception you choose could disrupt your Lactobacilli levels, making it harder for your body to fight off infection.
There’s no one-size-fits-all answer. But understanding how each method interacts with your microbiome can help you make more informed choices. For example:
Choosing contraception is about so much more than preventing pregnancy; it’s about protecting your long-term balance and wellbeing.
