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Operator
Good day, Ladies and gentlemen, welcome to the Natural Grocers second quarter fiscal year 2024, earnings conference call. (Operator Instructions) As a reminder, today's call is being recorded.
I'd now like to turn the conference over to Ms. Jessica Thiessen , Vice President and Treasurer for Natural Grocers.
Ms. Thiessen, you may begin.
Jessica Thiessen - VP and Treasurer
Good afternoon, and thank you for joining us, for the Natural Grocers, by Vitamin Cottage second quarter fiscal year 2024, earnings conference call.
On the call with me today are Kemper Isely, Co-President, and Todd Dissinger, Chief Financial Officer.
As a reminder, certain information provided during this conference call are forward looking statements based on current expectations and assumptions and are subject to risks and uncertainties. Actual results could differ materially from those described in the forward-looking statements due to a variety of factors, including the risks and uncertainties detailed in the Company's most recently filed Forms 10-Q and 10-K. The Company undertakes no obligation to update forward-looking statements.
Today's press release is available on the company's website and a recording of this call will be available on the website at investors.natural grocers.com
Now I will turn the call over to Kemper.
Kemper Isely - Chairman of the Board, Co-President
Thank you, Jessica, and good afternoon, everyone. Today I would like to highlight our second quarter financial results and speak to the key drivers of our performance. Then Todd will discuss the results in greater detail and review our updated fiscal year 2024 guidance.
The second quarter results were outstanding, as we delivered record quarterly sales margin expansion and significant earnings growth. Our performance reflects a continuation of the positive trends we experienced in recent quarters. Daily average comparable store sales accelerated to 7.5%, driven by a 3.9% increase in basket size, including item count growth and a 3.5% increase in customer traffic.
The sales comp on a two year basis was 10.2% and was the fifth consecutive quarter of strong two year comps. New stores also contributed to the sales growth. During the second quarter, we opened one new store and we are pleased with the performance of all four new stores opened in the last 12 months.
Strong sales growth, combined with effective expense management, generated operating leverage and drove a 34.6% increase in diluted earnings per share to $0.35. We believe that our strong sales growth over the last year is primarily attributable to three key drivers. Our differentiated business model, effective customer engagement and productivity initiatives. I will elaborate on each driver.
The first driver of accelerated sales is our differentiated business model, which sets us apart from our competitors in terms of our high product standards, affordable pricing and free science-based nutrition education. These disciplines have been core to Natural Grocers since our founding in 1955 and are increasingly relevant to today's consumers.
We carefully vet our natural and organic product offerings based upon rigorous product standards designed to support Human Health animal welfare in a more regenerative environment a few examples of our strict standards include selling only 100% certified organic proteins, only pasture raised dairy and only eggs from free range pasture raised chickens.
Our grocery peers may offer a limited selection of products with similar standards where as every Natural Grocers store only offers carefully vetted natural and organic products. Are care-fully embedded products are offered at affordable prices, providing customers a very compelling value proposition.
We strive to offer pricing that makes regenerative sustainable and healthier choices more affordable and accessible. We believe our pricing strategy coupled with our compelling rewards program, enable our customers to shop our stores on a regular basis for their groceries, dietary supplements and household essentials.
Our strong sales momentum through the second quarter reflects our continuing engagement with our loyal and resilient customer base. And our alignment with consumer trends. So who are our customers, Natural Grocers appeals to a diverse group of consumers. We believe that many consumers have a greater focus on health and wellness as a result of the pandemic, inflation over the past two years has increased consumer emphasis on value.
Our customers prioritize products with health and sustainability attributes and understand our differentiation in the market. Our core customers skews slightly older and is focused on a healthy lifespan. This group tends to have a higher household income and their spending has been more resilient in recent years. We also appeal to younger generations who prioritize health and sustainability and embrace Natural Grocers authenticity.
Second driver of accelerated sales is effective customer engagement through marketing initiatives and offer management. We continue to leverage. Our Empower rewards program is reflected in the net sales penetration of 78% up from 76% a year ago. We continually refine and enhance the personalization frequency and range of our Empower offers.
We also prioritize customer engagement through a convenient retail environment as well as a high level of customer service. Additionally, we provide extensive free science-based nutrition education programs and coaching in our stores, to help customers make informed health and nutrition choices.
The third driver of accelerated sales is productivity initiatives. We developed targeted local and regional marketing campaigns that accelerated sales growth in underperforming stores. We also implemented operational productivity initiatives that enabled us to streamline and automate certain in-store tasks.
Allowing our crew to devote more time to customer-facing activities to further enhance sales and customer service in our stores. Our differentiated business model relevance to consumer trends, customer engagement and productivity initiatives resulted in profitable sales growth over the past several quarters.
In closing, I would like to thank our good-for-you crew for their commitment to operational excellence and exceptional customer service that were instrumental in driving our results. We are fortunate to have crew who share an affinity for our founding principles and are dedicated to ensuring that our stores, operations and supply chain, reflect these values.
With that, I will turn our call over to Todd to discuss our financial results and guidance.
Todd Dissinger - Chief Financial Officer
Thank you, Kemper, and good afternoon. We are very pleased with our strong second quarter performance. Net sales increased 8.8% from the prior year period to $308.1 million. Daily average comparable store sales increased 7.5% and increased 10.2% on a two year basis.
Our daily average transaction size increased 3.9% about half of the transaction size comp was attributed to an increase in items per basket. The item count increase reflected a continuation of the improving trend we experienced over the past several quarters. Every major product category had an increase in item count.
The other half of the transaction size comp was attributed to product cost inflation. We estimate that annualized cost inflation for the second quarter was approximately 2%, which was down one percentage point from the previous quarter. Our daily average transaction count increased 3.5%. This marks our fifth consecutive quarter with positive customer traffic comps.
Sales growth was broad-based across product categories. Our strongest performing departments were meat, dairy and body care. The Dietary supplements. Sales comp was in the low single digits. Our branded products continue to gain share basket and accounted for 8.5% of total sales, up from 8.1% a year ago.
Gross margin increased 20 basis points to 29.3%, driven by store occupancy cost leverage, partially offset by lower product margin attributable to a lower supplement sales mix in the second quarter of fiscal 2023, we implemented several pricing and promotional strategies, which benefited the year-over-year margin improvement we experienced over the past several quarters. In the second quarter of 2024, we started to anniversary those benefits, resulting in more moderate margin improvement.
Store expenses increased 6.2% in the second quarter, primarily driven by higher compensation expenses, store expenses as a percentage of sales decreased 50 basis points, reflecting expense leverage as elevated sales more than offset higher labor costs.
Administrative expenses as a percentage of sales increased 10 basis points driven by higher compensation expenses. Net income was $8 million with diluted earnings per share of $0.35 in the second quarter. This compares to net income of $5.9 million or $0.26 of diluted earnings per share in the second quarter of last year. Adjusted EBITDA was $19.7 million in the second quarter.
Turning to the balance sheet and cash flow. We ended the second quarter in a strong financial position, including $11 million of cash and cash equivalents. We had $11.4 million in outstanding borrowings on our $75 million revolving credit facility.
During the first six months of fiscal 2024, we generated cash from operations of $36.8 million and invested $22.5 million in net capital expenditures, primarily for new and relocated stores, resulting in free cash flow of $14.3 million.
We are raising our fiscal 2024 guidance for daily average comparable store sales growth and diluted earnings per share. Our revised guidance includes the following, open four to six new stores relocate or remodel four to six stores achieve daily average comparable store sales growth between 4% and 6%, achieved diluted earnings per share between $1.08 and $1.18 and direct $30 million to $39 million towards capital expenditures to support our growth initiatives.
Our outlook reflects the first half results, operating trends and the current economic environment. Our expectation is that daily average comparable store sales will moderate in the second half of the year as we cycled stronger comps in the back half of fiscal 2023.
Our outlook anticipates that year-over-year gross margin will be about flat in the second half of the year as we will have cycled the benefit of several pricing and promotional strategies implemented last year.
Lastly, we expect store expenses as a percentage of sales to be relatively flat on a year-over-year basis.
In closing, we are very pleased with our second quarter results, which reflect a continuation of the positive trends we experienced in recent quarters. The strong sales growth combined with expense management generated operating leverage and yielded a 34.6% increase in diluted earnings per share.
We believe our carefully vetted offering of natural and organic products, coupled with our emphasis on value and always affordable pricing, differentiate us in the marketplace and continue to drive demand with health-conscious consumers.
With that, I would like to open up the lines for questions.
Thank you.
Operator
Scott Mushkin, R5 Capital.
Unidentified_Participant
This is Ryan on for Scott. Congrats on the performance. So I guess I had a few questions. What do you attribute your success to with your strong comp on In other words, like in the market, what do you think your initiatives are the most successful?
Kemper Isely - Chairman of the Board, Co-President
Well, we're very good at communicating with our customers on a weekly basis because of our loyalty program and we are getting 78% of our sales from those people that are on our loyalty program and we communicate with them approximately four times a week. And we have various promotions that resonate well with them and it drives for shopping and increases their basket.
But the other thing is that we have a model, -- a business model founded based on our five founding principles of nutrition, education, quality products, everyday, affordable pricing. Being engaged in our communities and taking care of our crew that also resonates with our customers and it's causing a lot of it makes it makes us have a very loyal customer base and is expanding our customer base.
Unidentified_Participant
Okay, great. That makes sense.
And then just the topic of DenTek do you feel as though it's impacting your business in any way? There was actually an article in the Journal this morning that said that those expectations are trying to continue their house and kind of maintain their weight, after being ozempic. And you feel as though those customers or those consumers will come to you?
Kemper Isely - Chairman of the Board, Co-President
I think it'll increase our customer base because people are looking for. Well, if you're if you're losing weight, you're looking for a way to lose weight and then you're losing looking for a way to keep it off and you, of course, want to be educated on on nutrition and how to take care of your body. And that's what we do very well at our stores.
Unidentified_Participant
And then finally, with your new stores, you opened one this quarter. What do you think is doing the best within that store?
Kemper Isely - Chairman of the Board, Co-President
You mean as far as which categories are doing investments for --
Unidentified_Participant
Yeah, which categories and just, which category?
Kemper Isely - Chairman of the Board, Co-President
Well, our grocery category is always our strongest category, but every category is doing well and perhaps towards dinner and successful overall in every category. So there isn't one particular Shining Star, it's pretty much Matt, and that are matching up to our own normal. new stores categories. -- So new category growth for each of each category.
And then of course, we've done a really good job reaching out to the community and getting good support in the community before the store opened. And after the store opened. I'm just giving out the word about our store being there and what we're about, so on and so forth.
Unidentified_Participant
All right.
Great.
That's all I have.
Kemper Isely - Chairman of the Board, Co-President
Thank you.
Operator
This concludes our question and answer session. I would like to turn the conference back over to Kemper for any closing remarks.
Kemper Isely - Chairman of the Board, Co-President
Thank you for joining us. We continue to be encouraged by our recent operating trends, and we are confident in our ability to drive growth and enhance value for all our stakeholders. Thank you and have a great day.
Operator
The conference has now concluded. Thank you for attending today's presentation. You may now disconnect.